From fc0f5c5c17f301cd87725a904ee3e4848b91a725 Mon Sep 17 00:00:00 2001 From: Felix Fischer Date: Wed, 1 Oct 2025 18:50:59 +0200 Subject: [PATCH 01/15] =?UTF-8?q?=F0=9F=93=9D=20Added=20quickstart=20noteb?= =?UTF-8?q?ook?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/notebooks/example.ipynb | 217 ++++++++++++++++++++++++++++++++++- 1 file changed, 216 insertions(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 24eab28..19d10f9 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -3,9 +3,224 @@ { "cell_type": "markdown", "metadata": {}, + "source": "# Quickstart `annbatch`" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "This notebook will walk you through the following steps:\n", + "1. How to convert an existing collection of `h5ad` files into `annbatch` format\n", + "2. How to load the converted dataset using `annbatch`" + ] + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "# Download an example dataset from CELLxGENE\n", + "!wget https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "## IMPORTANT: Configure zarrs\n", + "\n", + "This step is both required for converting existing `h5ad` files into `annbatch` format as well as for the data loading part." + ] + }, + { + "metadata": {}, + "cell_type": "code", "source": [ - "# Example notebook" + "import zarr\n", + "import zarrs # noqa\n", + "\n", + "zarr.config.set(\n", + " {\n", + " \"threading.max_workers\": 5,\n", + " \"codec_pipeline.path\": \"zarrs.ZarrsCodecPipeline\",\n", + " \"concurrency\": 4,\n", + " }\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "import warnings\n", + "\n", + "# Suppress zarr vlen-utf8 codec warnings\n", + "warnings.filterwarnings(\n", + " \"ignore\",\n", + " message=\"The codec `vlen-utf8` is currently not part in the Zarr format 3 specification.*\",\n", + " category=UserWarning,\n", + " module=\"zarr.codecs.vlen_utf8\",\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": "## Converting existing h5ad files into `annbatch` format" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "The conversion code will take care of the following things:\n", + "* Align the gene spaces across all datasets listed in `adata_paths`\n", + " * The gene spaces are aligned based on the gene names provided in the `var_names` field of the individual `AnnData` objects.\n", + " * If you want to subset to specific gene space, you can provide a list of gene names via the `var_subset` parameter.\n", + "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", + " * This is important for block-wise shuffling during data loading.\n", + " * This can be disabled by setting `shuffle=False`\n", + "* Shard the combined dataset across multiple datasets:\n", + " * The size of each shard can be controlled via the `n_obs_per_dataset` parameter.\n", + " * We recommend to choose a shard size that comfortably fits into system memory." ] + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "from arrayloaders import create_anndata_collection\n", + "\n", + "create_anndata_collection(\n", + " # List all the h5ad files you want to include in the collection\n", + " adata_paths=[\n", + " \"866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\",\n", + " ],\n", + " # Path to store the output collection\n", + " output_path=\"tahoe100_FULL\",\n", + " shuffle=True, # Whether to pre-shuffle the cells of the collection\n", + " n_obs_per_dataset=2_097_152, # Number of cells per dataset shard\n", + " var_subset=None, # Optionally subset the collection to a specific gene space\n", + " should_denseify=False,\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": "## Data loading example" + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "from pathlib import Path\n", + "\n", + "COLLECTION_PATH = Path(\"tahoe100_FULL/\")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "import anndata as ad\n", + "\n", + "from arrayloaders import ZarrSparseDataset\n", + "\n", + "ds = ZarrSparseDataset(\n", + " batch_size=4096, # Number of cells per yielded batch\n", + " chunk_size=256, # Number of cells to load from disk contiguously - default settings should work well\n", + " preload_nchunks=32, # Number of chunks to preload in the background + shuffle - default settings should work well\n", + ")\n", + "\n", + "# Add dataset that should be used for training\n", + "ds.add_anndatas(\n", + " [\n", + " ad.AnnData(\n", + " X=ad.io.sparse_dataset(zarr.open(p)[\"X\"]),\n", + " obs=ad.io.read_elem(zarr.open(p)[\"obs\"]),\n", + " )\n", + " for p in COLLECTION_PATH.glob(\"*.zarr\")\n", + " ],\n", + " obs_keys=\"cell_type\",\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "IMPORTANT:\n", + "* The `ZarrSparseDataset` yields batches of sparse tensors.\n", + "* The conversion to dense tensors should be done on the GPU, as shown in the example below.\n", + " * First call `.cuda()` and then `.to_dense()`\n", + " * E.g. `x = x.cuda().to_dense()`\n", + " * This is significantly faster than doing the dense conversion on the CPU.\n" + ] + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "# Iterate over dataloader\n", + "for batch in ds:\n", + " x, obs = batch\n", + " # Important: Convert to dense on GPU\n", + " x = x.cuda().to_dense()\n", + " # Feed data into your model\n", + " ..." + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": "## Optional: Extend an existing collection with a new dataset" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "You might want to extend an existing pre-shuffled collection with a new dataset.\n", + "This can be done using the `add_to_collection` function.\n", + "\n", + "This function will take care of shuffling the new dataset into the existing collection without having to re-shuffle the entire collection." + ] + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "from arrayloaders import add_to_collection\n", + "\n", + "add_to_collection(\n", + " adata_paths=[\n", + " \"866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\",\n", + " ],\n", + " output_path=\"tahoe100_FULL\",\n", + " read_full_anndatas=True, # This should be set to False if the new datasets DO NOT fit into memory\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": "", + "outputs": [], + "execution_count": null } ], "metadata": { From a003fa5bd1357a8a53ef7fc72030639e0b3cfc71 Mon Sep 17 00:00:00 2001 From: Felix Fischer Date: Mon, 6 Oct 2025 11:31:50 +0200 Subject: [PATCH 02/15] =?UTF-8?q?=F0=9F=8E=A8=20Added=20suggestions=20from?= =?UTF-8?q?=20@ilan-gold?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/notebooks/example.ipynb | 115 +++++++++++++++++------------------ 1 file changed, 55 insertions(+), 60 deletions(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 19d10f9..9543854 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -6,27 +6,29 @@ "source": "# Quickstart `annbatch`" }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": [ "This notebook will walk you through the following steps:\n", "1. How to convert an existing collection of `h5ad` files into `annbatch` format\n", - "2. How to load the converted dataset using `annbatch`" + "2. How to load the converted dataset using `annbatch`\n", + "3. Extend an existing collection with new datasets" ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "# Download an example dataset from CELLxGENE\n", - "!wget https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad" - ], - "outputs": [], - "execution_count": null + "!wget https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\n", + "!wget https://datasets.cellxgene.cziscience.com/f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad" + ] }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": [ "## IMPORTANT: Configure zarrs\n", "\n", @@ -34,26 +36,22 @@ ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "import zarr\n", "import zarrs # noqa\n", "\n", - "zarr.config.set(\n", - " {\n", - " \"threading.max_workers\": 5,\n", - " \"codec_pipeline.path\": \"zarrs.ZarrsCodecPipeline\",\n", - " \"concurrency\": 4,\n", - " }\n", - ")" - ], - "outputs": [], - "execution_count": null + "zarr.config.set({\"codec_pipeline.path\": \"zarrs.ZarrsCodecPipeline\"})" + ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "import warnings\n", "\n", @@ -64,21 +62,19 @@ " category=UserWarning,\n", " module=\"zarr.codecs.vlen_utf8\",\n", ")" - ], - "outputs": [], - "execution_count": null + ] }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": "## Converting existing h5ad files into `annbatch` format" }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": [ "The conversion code will take care of the following things:\n", - "* Align the gene spaces across all datasets listed in `adata_paths`\n", + "* Align (outer join) the gene spaces across all datasets listed in `adata_paths`\n", " * The gene spaces are aligned based on the gene names provided in the `var_names` field of the individual `AnnData` objects.\n", " * If you want to subset to specific gene space, you can provide a list of gene names via the `var_subset` parameter.\n", "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", @@ -90,46 +86,46 @@ ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "from arrayloaders import create_anndata_collection\n", "\n", "create_anndata_collection(\n", " # List all the h5ad files you want to include in the collection\n", - " adata_paths=[\n", - " \"866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\",\n", - " ],\n", + " adata_paths=[\"866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\", \"f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad\"],\n", " # Path to store the output collection\n", - " output_path=\"tahoe100_FULL\",\n", + " output_path=\"annbatch_collection\",\n", " shuffle=True, # Whether to pre-shuffle the cells of the collection\n", " n_obs_per_dataset=2_097_152, # Number of cells per dataset shard\n", " var_subset=None, # Optionally subset the collection to a specific gene space\n", " should_denseify=False,\n", ")" - ], - "outputs": [], - "execution_count": null + ] }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": "## Data loading example" }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "from pathlib import Path\n", "\n", - "COLLECTION_PATH = Path(\"tahoe100_FULL/\")" - ], - "outputs": [], - "execution_count": null + "COLLECTION_PATH = Path(\"annbatch_collection/\")" + ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "import anndata as ad\n", "\n", @@ -139,6 +135,7 @@ " batch_size=4096, # Number of cells per yielded batch\n", " chunk_size=256, # Number of cells to load from disk contiguously - default settings should work well\n", " preload_nchunks=32, # Number of chunks to preload in the background + shuffle - default settings should work well\n", + " preload_to_gpu=False, # If True, preloaded chunks are moved to GPU memory - requires enough GPU memory\n", ")\n", "\n", "# Add dataset that should be used for training\n", @@ -152,15 +149,13 @@ " ],\n", " obs_keys=\"cell_type\",\n", ")" - ], - "outputs": [], - "execution_count": null + ] }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": [ - "IMPORTANT:\n", + "**IMPORTANT:**\n", "* The `ZarrSparseDataset` yields batches of sparse tensors.\n", "* The conversion to dense tensors should be done on the GPU, as shown in the example below.\n", " * First call `.cuda()` and then `.to_dense()`\n", @@ -169,8 +164,10 @@ ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "# Iterate over dataloader\n", "for batch in ds:\n", @@ -179,18 +176,16 @@ " x = x.cuda().to_dense()\n", " # Feed data into your model\n", " ..." - ], - "outputs": [], - "execution_count": null + ] }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": "## Optional: Extend an existing collection with a new dataset" }, { - "metadata": {}, "cell_type": "markdown", + "metadata": {}, "source": [ "You might want to extend an existing pre-shuffled collection with a new dataset.\n", "This can be done using the `add_to_collection` function.\n", @@ -199,8 +194,10 @@ ] }, { - "metadata": {}, "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "from arrayloaders import add_to_collection\n", "\n", @@ -208,19 +205,17 @@ " adata_paths=[\n", " \"866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\",\n", " ],\n", - " output_path=\"tahoe100_FULL\",\n", + " output_path=\"annbatch_collection\",\n", " read_full_anndatas=True, # This should be set to False if the new datasets DO NOT fit into memory\n", ")" - ], - "outputs": [], - "execution_count": null + ] }, { - "metadata": {}, "cell_type": "code", - "source": "", + "execution_count": null, + "metadata": {}, "outputs": [], - "execution_count": null + "source": [] } ], "metadata": { From a8afc729c12d5a85eea703aa3900d690fb25d3c1 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:04 +0200 Subject: [PATCH 03/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 9543854..449e192 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -10,9 +10,9 @@ "metadata": {}, "source": [ "This notebook will walk you through the following steps:\n", - "1. How to convert an existing collection of `h5ad` files into `annbatch` format\n", - "2. How to load the converted dataset using `annbatch`\n", - "3. Extend an existing collection with new datasets" + "1. How to convert an existing collection of `anndata` files into a shuffled, zarr-based, collection of `anndata` datasets\n", + "2. How to load the converted collection using `annbatch`\n", + "3. Extend an existing collection with new `anndata` datasets" ] }, { From e472723c74527935323cfd3681d3f5a511c6c44b Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:11 +0200 Subject: [PATCH 04/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 449e192..e3da8d4 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -21,7 +21,7 @@ "metadata": {}, "outputs": [], "source": [ - "# Download an example dataset from CELLxGENE\n", + "# Download two example datasets from CELLxGENE\n", "!wget https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\n", "!wget https://datasets.cellxgene.cziscience.com/f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad" ] From acce4e9c58c494fa6fbdc398a165e1a8a3493bc4 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:19 +0200 Subject: [PATCH 05/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index e3da8d4..2da82af 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -32,7 +32,7 @@ "source": [ "## IMPORTANT: Configure zarrs\n", "\n", - "This step is both required for converting existing `h5ad` files into `annbatch` format as well as for the data loading part." + "This step is both required for converting existing `anndata` files into a performant, shuffled collection of datasets for mini batch loading" ] }, { From 23cf14b841ef3a9b258ec323ad823adc84d08cbd Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:27 +0200 Subject: [PATCH 06/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 2da82af..c0e9f3d 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -67,7 +67,7 @@ { "cell_type": "markdown", "metadata": {}, - "source": "## Converting existing h5ad files into `annbatch` format" + "source": "## Converting existing `anndata` files into a shuffled collection" }, { "cell_type": "markdown", From c1df1fc98cf0a7a2a7bb9f3f92673b4b9725eae0 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:34 +0200 Subject: [PATCH 07/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index c0e9f3d..1ceb2eb 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -75,7 +75,7 @@ "source": [ "The conversion code will take care of the following things:\n", "* Align (outer join) the gene spaces across all datasets listed in `adata_paths`\n", - " * The gene spaces are aligned based on the gene names provided in the `var_names` field of the individual `AnnData` objects.\n", + " * The gene spaces are outer-joined based on the gene names provided in the `var_names` field of the individual `AnnData` objects.\n", " * If you want to subset to specific gene space, you can provide a list of gene names via the `var_subset` parameter.\n", "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", " * This is important for block-wise shuffling during data loading.\n", From ae20e021bd8bda564b7b1ac333106de71eb5e20c Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:47 +0200 Subject: [PATCH 08/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 1ceb2eb..54b70b0 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -79,7 +79,6 @@ " * If you want to subset to specific gene space, you can provide a list of gene names via the `var_subset` parameter.\n", "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", " * This is important for block-wise shuffling during data loading.\n", - " * This can be disabled by setting `shuffle=False`\n", "* Shard the combined dataset across multiple datasets:\n", " * The size of each shard can be controlled via the `n_obs_per_dataset` parameter.\n", " * We recommend to choose a shard size that comfortably fits into system memory." From d4c5327fb7cee68cb787a521f51871e1078620e4 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:49:59 +0200 Subject: [PATCH 09/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 54b70b0..66beeef 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -79,7 +79,7 @@ " * If you want to subset to specific gene space, you can provide a list of gene names via the `var_subset` parameter.\n", "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", " * This is important for block-wise shuffling during data loading.\n", - "* Shard the combined dataset across multiple datasets:\n", + "* Shuffle the input files across multiple output datasets:\n", " * The size of each shard can be controlled via the `n_obs_per_dataset` parameter.\n", " * We recommend to choose a shard size that comfortably fits into system memory." ] From f0ebccc0621752bb68c114b2e9a566d0dab02aec Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:50:07 +0200 Subject: [PATCH 10/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 66beeef..b7afb0e 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -80,7 +80,7 @@ "* Shuffle the cells across all datasets (this works on larger than memory datasets as well).\n", " * This is important for block-wise shuffling during data loading.\n", "* Shuffle the input files across multiple output datasets:\n", - " * The size of each shard can be controlled via the `n_obs_per_dataset` parameter.\n", + " * The size of each individual output dataset can be controlled via the `n_obs_per_dataset` parameter.\n", " * We recommend to choose a shard size that comfortably fits into system memory." ] }, From 2bc5031d2f1c4ce2895d5821aa2adf9143895732 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:50:14 +0200 Subject: [PATCH 11/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index b7afb0e..6575753 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -81,7 +81,7 @@ " * This is important for block-wise shuffling during data loading.\n", "* Shuffle the input files across multiple output datasets:\n", " * The size of each individual output dataset can be controlled via the `n_obs_per_dataset` parameter.\n", - " * We recommend to choose a shard size that comfortably fits into system memory." + " * We recommend to choose a dataset size that comfortably fits into system memory." ] }, { From 1e7d03c9e678e08b8b2799bd3d1e33043012e8a5 Mon Sep 17 00:00:00 2001 From: Felix Fischer <47145207+felix0097@users.noreply.github.com> Date: Mon, 6 Oct 2025 15:50:24 +0200 Subject: [PATCH 12/15] Apply suggestion from @ilan-gold Co-authored-by: Ilan Gold --- docs/notebooks/example.ipynb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 6575753..51764f5 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -131,10 +131,10 @@ "from arrayloaders import ZarrSparseDataset\n", "\n", "ds = ZarrSparseDataset(\n", - " batch_size=4096, # Number of cells per yielded batch\n", - " chunk_size=256, # Number of cells to load from disk contiguously - default settings should work well\n", - " preload_nchunks=32, # Number of chunks to preload in the background + shuffle - default settings should work well\n", - " preload_to_gpu=False, # If True, preloaded chunks are moved to GPU memory - requires enough GPU memory\n", + " batch_size=4096, # Total number of obs per yielded batch\n", + " chunk_size=256, # Number of obs to load from disk contiguously - default settings should work well\n", + " preload_nchunks=32, # Number of chunks to preload + shuffle - default settings should work well\n", + " preload_to_gpu=False, # If True, preloaded chunks are moved to GPU memory via `cupy`, which can put more pressure on GPU memory but will accelerate loading ~20%\n", ")\n", "\n", "# Add dataset that should be used for training\n", From aca5bb054e5e0bfc19155119459f53d6b59cbe17 Mon Sep 17 00:00:00 2001 From: ilan-gold Date: Wed, 8 Oct 2025 15:25:55 +0200 Subject: [PATCH 13/15] fix: small doc fixes --- docs/index.md | 3 +-- docs/notebooks/example.ipynb | 24 ++++++++++++++++-------- docs/notebooks/index.md | 8 ++++++++ 3 files changed, 25 insertions(+), 10 deletions(-) create mode 100644 docs/notebooks/index.md diff --git a/docs/index.md b/docs/index.md index dd61acc..aad5984 100644 --- a/docs/index.md +++ b/docs/index.md @@ -117,6 +117,5 @@ api.md changelog.md contributing.md references.md - -notebooks/example +notebooks/index ``` diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 51764f5..6760cc3 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -3,7 +3,9 @@ { "cell_type": "markdown", "metadata": {}, - "source": "# Quickstart `annbatch`" + "source": [ + "# Quickstart `annbatch`" + ] }, { "cell_type": "markdown", @@ -30,7 +32,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## IMPORTANT: Configure zarrs\n", + "**IMPORTANT**: Configure zarrs\n", "\n", "This step is both required for converting existing `anndata` files into a performant, shuffled collection of datasets for mini batch loading" ] @@ -67,7 +69,9 @@ { "cell_type": "markdown", "metadata": {}, - "source": "## Converting existing `anndata` files into a shuffled collection" + "source": [ + "## Converting existing `anndata` files into a shuffled collection" + ] }, { "cell_type": "markdown", @@ -90,7 +94,7 @@ "metadata": {}, "outputs": [], "source": [ - "from arrayloaders import create_anndata_collection\n", + "from annbatch import create_anndata_collection\n", "\n", "create_anndata_collection(\n", " # List all the h5ad files you want to include in the collection\n", @@ -107,7 +111,9 @@ { "cell_type": "markdown", "metadata": {}, - "source": "## Data loading example" + "source": [ + "## Data loading example" + ] }, { "cell_type": "code", @@ -128,7 +134,7 @@ "source": [ "import anndata as ad\n", "\n", - "from arrayloaders import ZarrSparseDataset\n", + "from annbatch import ZarrSparseDataset\n", "\n", "ds = ZarrSparseDataset(\n", " batch_size=4096, # Total number of obs per yielded batch\n", @@ -180,7 +186,9 @@ { "cell_type": "markdown", "metadata": {}, - "source": "## Optional: Extend an existing collection with a new dataset" + "source": [ + "## Optional: Extend an existing collection with a new dataset" + ] }, { "cell_type": "markdown", @@ -198,7 +206,7 @@ "metadata": {}, "outputs": [], "source": [ - "from arrayloaders import add_to_collection\n", + "from annbatch import add_to_collection\n", "\n", "add_to_collection(\n", " adata_paths=[\n", diff --git a/docs/notebooks/index.md b/docs/notebooks/index.md new file mode 100644 index 0000000..de485bf --- /dev/null +++ b/docs/notebooks/index.md @@ -0,0 +1,8 @@ +# Notebooks + +```{toctree} +:hidden: true +:maxdepth: 1 + +example +``` From ef2545ca4ca505bcca8755b500994ff256378546 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Thu, 9 Oct 2025 10:32:53 +0000 Subject: [PATCH 14/15] chore: make notebook work with #62 --- docs/notebooks/example.ipynb | 2396 +++++++++++++++++++++++++++++++++- 1 file changed, 2373 insertions(+), 23 deletions(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 6760cc3..726da4b 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -14,14 +14,49 @@ "This notebook will walk you through the following steps:\n", "1. How to convert an existing collection of `anndata` files into a shuffled, zarr-based, collection of `anndata` datasets\n", "2. How to load the converted collection using `annbatch`\n", - "3. Extend an existing collection with new `anndata` datasets" + "3. Extend an existing collection with new `anndata` datasets\n", + "\n", + "To use this notebook, install the extras:\n", + "\n", + "```\n", + "pip install annbatch[zarrs, torch]\n", + "```" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "--2025-10-09 09:43:19-- https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\n", + "Resolving datasets.cellxgene.cziscience.com (datasets.cellxgene.cziscience.com)... 18.64.79.73, 18.64.79.80, 18.64.79.109, ...\n", + "Connecting to datasets.cellxgene.cziscience.com (datasets.cellxgene.cziscience.com)|18.64.79.73|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 773247972 (737M) [binary/octet-stream]\n", + "Saving to: ‘866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad’\n", + "\n", + "866d7d5e-436b-4dbd- 100%[===================>] 737.43M 398MB/s in 1.9s \n", + "\n", + "2025-10-09 09:43:21 (398 MB/s) - ‘866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad’ saved [773247972/773247972]\n", + "\n", + "--2025-10-09 09:43:22-- https://datasets.cellxgene.cziscience.com/f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad\n", + "Resolving datasets.cellxgene.cziscience.com (datasets.cellxgene.cziscience.com)... 18.64.79.73, 18.64.79.80, 18.64.79.72, ...\n", + "Connecting to datasets.cellxgene.cziscience.com (datasets.cellxgene.cziscience.com)|18.64.79.73|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 1631759823 (1.5G) [binary/octet-stream]\n", + "Saving to: ‘f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad’\n", + "\n", + "f81463b8-4986-4904- 100%[===================>] 1.52G 425MB/s in 3.9s \n", + "\n", + "2025-10-09 09:43:26 (403 MB/s) - ‘f81463b8-4986-4904-a0ea-20ff02cbb317.h5ad’ saved [1631759823/1631759823]\n", + "\n" + ] + } + ], "source": [ "# Download two example datasets from CELLxGENE\n", "!wget https://datasets.cellxgene.cziscience.com/866d7d5e-436b-4dbd-b7c1-7696487d452e.h5ad\n", @@ -39,9 +74,20 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "import zarr\n", "import zarrs # noqa\n", @@ -51,7 +97,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -90,11 +136,1134 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/mnt/volume/arrayloaders/src/annbatch/io.py:214: UserWarning: Some anndatas have raw and others do not, consider deleting raw via transform_input_adata\n", + " adata_concat = _lazy_load_with_obs_var_in_memory(adata_paths)\n", + " 0%| | 0/1 [00:00 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "csr_matrix \n", + " Coords\tValues\n", + " (0, 6381)\t0.0\n", + " (0, 7766)\t0.0\n", + " (0, 8748)\t0.0\n", + " (0, 8975)\t0.0\n", + " (0, 12475)\t0.0\n", + " (0, 12479)\t0.0\n", + " (0, 12481)\t0.0\n", + " (0, 13841)\t0.0\n", + " (0, 14274)\t0.0\n", + " (0, 14909)\t0.0\n", + " (0, 16128)\t0.0\n", + " (0, 17261)\t0.0\n", + " (0, 17271)\t0.0\n", + " (0, 17497)\t0.0\n", + " (0, 17896)\t0.0\n", + " (0, 18254)\t0.0\n", + " (0, 18515)\t0.0\n", + " (0, 18518)\t0.0\n", + " (0, 18532)\t0.0\n", + " (0, 18743)\t0.0\n", + " (0, 18745)\t0.0\n", + " (0, 18769)\t0.0\n", + " (0, 18790)\t0.0\n", + " (0, 18794)\t0.0\n", + " (0, 18807)\t0.0\n", + " :\t:\n", + " (986, 36077)\t0.0\n", + " (986, 36088)\t0.0\n", + " (986, 36101)\t0.0\n", + " (986, 36114)\t0.0\n", + " (986, 36120)\t0.0\n", + " (986, 36133)\t0.0\n", + " (986, 36140)\t0.0\n", + " (986, 36143)\t0.0\n", + " (986, 36149)\t0.0\n", + " (986, 36158)\t0.0\n", + " (986, 36179)\t0.0\n", + " (986, 36211)\t0.0\n", + " (986, 36214)\t0.0\n", + " (986, 36224)\t0.0\n", + " (986, 36244)\t0.0\n", + " (986, 36269)\t0.0\n", + " (986, 36285)\t0.0\n", + " (986, 36310)\t0.0\n", + " (986, 36318)\t0.0\n", + " (986, 36363)\t0.0\n", + " (986, 36373)\t0.0\n", + " (986, 35974)\t1.443677544593811\n", + " (986, 36296)\t1.443677544593811\n", + " (986, 36393)\t2.011228561401367\n", + " (986, 36075)\t1.443677544593811 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "dataframe reference_genome \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 GRCh38 \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 GRCh38 \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 GRCh38 \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 GRCh38 \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 GRCh38 \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 GRCh38 \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 GRCh38 \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 GRCh38 \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " gene_annotation_version \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 v98 \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 v98 \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 v98 \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 v98 \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 v98 \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 v98 \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 v98 \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 v98 \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " alignment_software \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 Cell Ranger count v7.1.0 \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 Cell Ranger count v7.1.0 \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 Cell Ranger count v7.1.0 \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 Cell Ranger count v7.1.0 \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " intronic_reads_counted \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 yes \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 yes \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 yes \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 yes \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 yes \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 yes \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 yes \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 yes \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " donor_id donor_age \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 BCM_22_0698 1 day \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 MMD_22_16860 60 years \n", + "CCACACTGTGGGCTTC-1-01_OM donor-TREE NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 BCM_23_1430 >89 years \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 BCM_22_0890 64 years \n", + "... ... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 MMD_23_17738 10 years \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 BCM_22_0698 1 day \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 BCM_23_0313 60 years \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 BCM_22_0458 25 years \n", + "CAACCTCAGTTGAATG-1-05_OM donor-PINK NaN \n", + "\n", + " self_reported_ethnicity_ontology_term_id \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 HANCESTRO:0005 \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 HANCESTRO:0568 \n", + "CCACACTGTGGGCTTC-1-01_OM HANCESTRO:0005 \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 HANCESTRO:0568 \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 HANCESTRO:0487 \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 HANCESTRO:0568 \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 HANCESTRO:0005 \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 HANCESTRO:0005 \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 HANCESTRO:0014 \n", + "CAACCTCAGTTGAATG-1-05_OM HANCESTRO:0568 \n", + "\n", + " donor_cause_of_death \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 unknown \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 unknown \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 unknown \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 unknown \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 unknown \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 unknown \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 unknown \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 unknown \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " donor_living_at_sample_collection \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 False \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 False \n", + "CCACACTGTGGGCTTC-1-01_OM True \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 False \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 False \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 False \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 False \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 False \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 False \n", + "CAACCTCAGTTGAATG-1-05_OM True \n", + "\n", + " sample_id \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 356c1cec-5dfc-4ed4-b07d-2f4b09dbc260 \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 01f33d4c-77df-4e82-b8c0-62d8c11a6e49 \n", + "CCACACTGTGGGCTTC-1-01_OM NaN \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 3306e8fd-b8c5-4d15-aac1-b31daa9e86b7 \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 02be6452-fe86-4589-84a2-cbb26954a76f \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 27848b53-eddb-44d6-894f-070488287fc2 \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 e322b3ae-fdee-462a-a4b3-37009212d7ed \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 f768fecc-f180-420c-9b86-672ad0233e18 \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 654adbbe-18f1-42ea-944b-8aa5f5848567 \n", + "CAACCTCAGTTGAATG-1-05_OM NaN \n", + "\n", + " ... mapped_reference_annotation \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 ... NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 ... NaN \n", + "CCACACTGTGGGCTTC-1-01_OM ... GENCODE 32 \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 ... NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 ... NaN \n", + "... ... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 ... NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 ... NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 ... NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 ... NaN \n", + "CAACCTCAGTTGAATG-1-05_OM ... GENCODE 32 \n", + "\n", + " sample_uuid \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM e1abc275-33f0-4198-8b08-c71f82d1fbd6 \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 1fc35617-2b40-498b-9060-4f0a911ae941 \n", + "\n", + " sample_derivation_process \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM dissection \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM dissection \n", + "\n", + " sample_source \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM Brigham and Women's Hospital \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM Brigham and Women's Hospital \n", + "\n", + " donor_BMI_at_collection \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM 59.7 \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 46.9 \n", + "\n", + " suspension_dissociation_reagent \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM Cytoplasmic cell lysis buffer \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM Cytoplasmic cell lysis buffer \n", + "\n", + " suspension_dissociation_time \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM 20 minute \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 20 minute \n", + "\n", + " library_uuid \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM 20027346-e846-46db-91c7-0574419aedda \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 4c67c43b-e36c-4efc-8469-cd9619280c98 \n", + "\n", + " library_starting_quantity \\\n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM 10000 nuclei \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 10000 nuclei \n", + "\n", + " leiden_scVI \n", + "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", + "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", + "CCACACTGTGGGCTTC-1-01_OM 4 \n", + "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", + "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", + "... ... \n", + "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", + "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", + "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", + "CAACCTCAGTTGAATG-1-05_OM 7 \n", + "\n", + "[171792 rows x 61 columns] obs {}\n", + "string-array ['3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1'\n", + " '3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1' 'CCACACTGTGGGCTTC-1-01_OM' ...\n", + " '3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1'\n", + " '3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1' 'CAACCTCAGTTGAATG-1-05_OM'] _index {}\n", + "categorical ['GRCh38', 'GRCh38', NaN, 'GRCh38', 'GRCh38', ..., 'GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', NaN]\n", + "Length: 171792\n", + "Categories (1, object): ['GRCh38'] reference_genome {}\n", + "array [ 0 0 -1 ... 0 0 -1] codes {}\n", + "string-array ['GRCh38'] categories {}\n", + "categorical ['v98', 'v98', NaN, 'v98', 'v98', ..., 'v98', 'v98', 'v98', 'v98', NaN]\n", + "Length: 171792\n", + "Categories (1, object): ['v98'] gene_annotation_version {}\n", + "array [ 0 0 -1 ... 0 0 -1] codes {}\n", + "string-array ['v98'] categories {}\n", + "categorical ['Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN, 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', ..., 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN]\n", + "Length: 171792\n", + "Categories (2, object): ['Cell Ranger count v7.0.1', 'Cell Ranger count v7.1.0'] alignment_software {}\n", + "array [ 1 1 -1 ... 1 1 -1] codes {}\n", + "string-array ['Cell Ranger count v7.0.1' 'Cell Ranger count v7.1.0'] categories {}\n", + "categorical ['yes', 'yes', NaN, 'yes', 'yes', ..., 'yes', 'yes', 'yes', 'yes', NaN]\n", + "Length: 171792\n", + "Categories (1, object): ['yes'] intronic_reads_counted {}\n", + "array [ 0 0 -1 ... 0 0 -1] codes {}\n", + "string-array ['yes'] categories {}\n", + "categorical ['BCM_22_0698', 'MMD_22_16860', 'donor-TREE', 'BCM_23_1430', 'BCM_22_0890', ..., 'MMD_23_17738', 'BCM_22_0698', 'BCM_23_0313', 'BCM_22_0458', 'donor-PINK']\n", + "Length: 171792\n", + "Categories (71, object): ['BCM_21_0948', 'BCM_22_0183', 'BCM_22_0200', 'BCM_22_0396', ..., 'donor-SILK', 'donor-TIME', 'donor-TREE', 'donor-ZONE'] donor_id {}\n", + "array [ 7 33 69 ... 15 5 66] codes {}\n", + "string-array ['BCM_21_0948' 'BCM_22_0183' 'BCM_22_0200' 'BCM_22_0396' 'BCM_22_0434'\n", + " 'BCM_22_0458' 'BCM_22_0500' 'BCM_22_0698' 'BCM_22_0769' 'BCM_22_0784'\n", + " 'BCM_22_0849' 'BCM_22_0890' 'BCM_22_0896' 'BCM_23_0131' 'BCM_23_0231'\n", + " 'BCM_23_0313' 'BCM_23_0334' 'BCM_23_0358' 'BCM_23_0491' 'BCM_23_0574'\n", + " 'BCM_23_1401' 'BCM_23_1430' 'BCM_23_1448' 'Hu13' 'Hu0218' 'Hu0220'\n", + " 'Hu0222' 'Hu0235' 'MMD_19_D005' 'MMD_19_D008' 'MMD_22_13066'\n", + " 'MMD_22_14307' 'MMD_22_16608' 'MMD_22_16860' 'MMD_22_17017'\n", + " 'MMD_22_17464' 'MMD_22_17939' 'MMD_22_20137' 'MMD_22_20357'\n", + " 'MMD_22_20372' 'MMD_22_21878' 'MMD_22_25357' 'MMD_22_33472'\n", + " 'MMD_22_34032' 'MMD_22_37089' 'MMD_22_37117' 'MMD_22_38029'\n", + " 'MMD_22_38453' 'MMD_23_01524' 'MMD_23_02177' 'MMD_23_17738'\n", + " 'MMD_23_21999' 'donor-APEX' 'donor-BLUE' 'donor-BOAT' 'donor-CORK'\n", + " 'donor-COST' 'donor-DOVE' 'donor-DOWN' 'donor-GOLD' 'donor-KEYS'\n", + " 'donor-KISS' 'donor-LACE' 'donor-OATS' 'donor-PASS' 'donor-PIKE'\n", + " 'donor-PINK' 'donor-SILK' 'donor-TIME' 'donor-TREE' 'donor-ZONE'] categories {}\n", + "categorical ['1 day', '60 years', NaN, '>89 years', '64 years', ..., '10 years', '1 day', '60 years', '25 years', NaN]\n", + "Length: 171792\n", + "Categories (31, object): ['1 day', '10 years', '11 years', '16 years', ..., '81 years', '82 years', '86 years', '>89 years'] donor_age {}\n", + "array [ 0 17 -1 ... 17 6 -1] codes {}\n", + "string-array ['1 day' '10 years' '11 years' '16 years' '17 years' '21 years' '25 years'\n", + " '27 years' '30 years' '32 years' '34 years' '43 years' '46 years'\n", + " '47 years' '50 years' '53 years' '58 years' '60 years' '62 years'\n", + " '63 years' '64 years' '65 years' '68 years' '69 years' '71 years'\n", + " '72 years' '77 years' '81 years' '82 years' '86 years' '>89 years'] categories {}\n", + "categorical ['HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0487', ..., 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0005', 'HANCESTRO:0014', 'HANCESTRO:0568']\n", + "Length: 171792\n", + "Categories (6, object): ['HANCESTRO:0005', 'HANCESTRO:0006', 'HANCESTRO:0014', 'HANCESTRO:0487', 'HANCESTRO:0568', 'unknown'] self_reported_ethnicity_ontology_term_id {}\n", + "array [0 4 0 ... 0 2 4] codes {}\n", + "string-array ['HANCESTRO:0005' 'HANCESTRO:0006' 'HANCESTRO:0014' 'HANCESTRO:0487'\n", + " 'HANCESTRO:0568' 'unknown'] categories {}\n", + "categorical ['unknown', 'unknown', NaN, 'unknown', 'unknown', ..., 'unknown', 'unknown', 'unknown', 'unknown', NaN]\n", + "Length: 171792\n", + "Categories (5, object): ['Coronary Artery Disease', 'Malignant Neoplasm', 'Meningeal Sarcoma', 'Septicemia', 'unknown'] donor_cause_of_death {}\n", + "array [ 4 4 -1 ... 4 4 -1] codes {}\n", + "string-array ['Coronary Artery Disease' 'Malignant Neoplasm' 'Meningeal Sarcoma'\n", + " 'Septicemia' 'unknown'] categories {}\n", + "categorical ['False', 'False', 'True', 'False', 'False', ..., 'False', 'False', 'False', 'False', 'True']\n", + "Length: 171792\n", + "Categories (2, object): ['False', 'True'] donor_living_at_sample_collection {}\n", + "array [0 0 1 ... 0 0 1] codes {}\n", + "string-array ['False' 'True'] categories {}\n", + "categorical ['356c1cec-5dfc-4ed4-b07d-2f4b09dbc260', '01f33d4c-77df-4e82-b8c0-62d8c11a6e49', NaN, '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7', '02be6452-fe86-4589-84a2-cbb26954a76f', ..., '27848b53-eddb-44d6-894f-070488287fc2', 'e322b3ae-fdee-462a-a4b3-37009212d7ed', 'f768fecc-f180-420c-9b86-672ad0233e18', '654adbbe-18f1-42ea-944b-8aa5f5848567', NaN]\n", + "Length: 171792\n", + "Categories (74, object): ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49', '01ffac9d-c058-47a0-969a-cb8fb51ffd03', '02be6452-fe86-4589-84a2-cbb26954a76f', '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce', ..., 'ed6fd53b-c1c3-49db-b1bb-112362a63b08', 'f86e512c-166d-41fc-b41c-b7baf70709a5', 'f768fecc-f180-420c-9b86-672ad0233e18', 'f932e7b5-1e6e-435d-8ad0-f340287da943'] sample_id {}\n", + "array [26 0 -1 ... 72 28 -1] codes {}\n", + "string-array ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49'\n", + " '01ffac9d-c058-47a0-969a-cb8fb51ffd03'\n", + " '02be6452-fe86-4589-84a2-cbb26954a76f'\n", + " '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce'\n", + " '5a2a6a3c-8f15-4eab-b2d1-7a6082659a83'\n", + " '5ae43655-e166-4c87-a0fd-13ee2eb525fc'\n", + " '5b839bc9-40f6-4b83-a039-2c424c917971'\n", + " '6a0b4dbd-5147-40ea-998a-3d578ae97d11'\n", + " '6fa3060a-d2b5-4cef-893f-f0b1f523ecc1'\n", + " '8e799a46-d8e2-4e72-a483-414168d778b5'\n", + " '9bc800be-b52f-485e-935b-b5bdda9fc5b8'\n", + " '12b49488-2f2d-4626-bffa-94aee3877981'\n", + " '24d12edd-fd54-4f44-9d21-63ee3c6fc807'\n", + " '25cc7497-b4b6-40e4-88ef-c0a2fe56a3ad'\n", + " '26bf8386-4a13-4fbc-8ff3-e85230a443a3'\n", + " '51e6ba30-757c-4c86-8492-16844de41645'\n", + " '54eb2056-e459-4edb-8bc8-d6adba201d61'\n", + " '55c1fb02-40ca-462c-8578-9196e3c83f89'\n", + " '64fff8e1-8db7-42e4-85df-b76ab1727414'\n", + " '67d22e15-0d05-4c65-bda4-9cb350949266'\n", + " '70df48a7-3d69-46e7-bacd-cdebc9bb6298'\n", + " '87ce0e14-0df9-4d53-99ba-9f1ebca7de9f'\n", + " '90b737c6-9ac7-4f8c-9efc-465a67874a63'\n", + " '136c4a3b-4502-4e7b-8851-fe332faf844c'\n", + " '242cabad-f81d-4fd7-8df7-fe0b318b6c34'\n", + " '245f8d19-2496-4fc0-953c-e202e74397a7'\n", + " '356c1cec-5dfc-4ed4-b07d-2f4b09dbc260'\n", + " '616d8f67-6128-4f7a-b2b3-8205f3d7d72d'\n", + " '654adbbe-18f1-42ea-944b-8aa5f5848567'\n", + " '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7'\n", + " '4722f3bd-2909-4026-b0b9-c471f4455658'\n", + " '9383cb3d-f39c-48c7-b0d6-6cfc26307523'\n", + " '16565f49-122b-4ae2-93b2-c772d76fa697'\n", + " '27848b53-eddb-44d6-894f-070488287fc2'\n", + " '46737bca-3ca2-451d-96fb-ebb433159f41'\n", + " '47201e9a-732d-4bfa-9279-2dea84738e2b'\n", + " '71357c06-8ba6-4b26-bd1a-531c84a9c589'\n", + " '91523cbf-a9f1-4451-8dec-53528db17ca0'\n", + " '632242f1-c6e3-4e8e-926e-c4973fd4e695'\n", + " '717599fd-3926-428e-be6a-a959904b7c1a'\n", + " '994416c8-9bc5-4c1c-9d7c-379d4b53b573'\n", + " '4826577c-c1a3-4c38-bb75-fdce5e6bec62'\n", + " '5586185c-a422-4441-a069-8bc8c652a347'\n", + " '76993467-f2ba-47ff-a967-fa5fbd373f81'\n", + " 'a2b49712-d112-443c-b144-51bf0c54875e'\n", + " 'a9df5458-8c11-4e0b-a3a5-aea273628f77'\n", + " 'a77bec3b-125a-4e1e-9559-739a1adb2e6b'\n", + " 'a89c72dd-c1bf-4029-95d1-b536fb1d71fc'\n", + " 'a3221835-bb93-41c7-a346-2e865b7ab0f4'\n", + " 'ac44c485-ca45-4d66-97fe-6e57b5f2d596'\n", + " 'ae8cde23-b13a-4d9c-80c3-7ea83ee3c9c1'\n", + " 'b0f3f8b7-7f1e-4f5b-95e1-bffc6768706e'\n", + " 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'f932e7b5-1e6e-435d-8ad0-f340287da943'] categories {}\n", + "categorical ['frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', ..., 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing']\n", + "Length: 171792\n", + "Categories (2, object): ['flash-freezing', 'frozen in liquid nitrogen'] sample_preservation_method {}\n", + "array [1 1 0 ... 1 1 0] codes {}\n", + "string-array ['flash-freezing' 'frozen in liquid nitrogen'] categories {}\n", + "categorical ['UBERON:0019207', 'UBERON:0019207', 'UBERON:0014454', 'UBERON:0019207', 'UBERON:0019207', ..., 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0014454']\n", + "Length: 171792\n", + "Categories (3, object): ['UBERON:0014454', 'UBERON:0014455', 'UBERON:0019207'] tissue_ontology_term_id {}\n", + "array [2 2 0 ... 2 2 0] codes {}\n", + "string-array ['UBERON:0014454' 'UBERON:0014455' 'UBERON:0019207'] categories {}\n", + "categorical ['HsapDv:0000262', 'HsapDv:0000154', 'HsapDv:0000160', 'HsapDv:0000274', 'HsapDv:0000158', ..., 'HsapDv:0000104', 'HsapDv:0000262', 'HsapDv:0000154', 'HsapDv:0000119', 'HsapDv:0000129']\n", + "Length: 171792\n", + "Categories (40, object): ['HsapDv:0000104', 'HsapDv:0000105', 'HsapDv:0000110', 'HsapDv:0000111', ..., 'HsapDv:0000208', 'HsapDv:0000212', 'HsapDv:0000262', 'HsapDv:0000274'] development_stage_ontology_term_id {}\n", + "array [38 24 29 ... 24 6 13] codes {}\n", + "string-array ['HsapDv:0000104' 'HsapDv:0000105' 'HsapDv:0000110' 'HsapDv:0000111'\n", + " 'HsapDv:0000112' 'HsapDv:0000115' 'HsapDv:0000119' 'HsapDv:0000120'\n", + " 'HsapDv:0000121' 'HsapDv:0000122' 'HsapDv:0000124' 'HsapDv:0000126'\n", + " 'HsapDv:0000128' 'HsapDv:0000129' 'HsapDv:0000131' 'HsapDv:0000135'\n", + " 'HsapDv:0000137' 'HsapDv:0000140' 'HsapDv:0000141' 'HsapDv:0000144'\n", + " 'HsapDv:0000145' 'HsapDv:0000147' 'HsapDv:0000148' 'HsapDv:0000152'\n", + " 'HsapDv:0000154' 'HsapDv:0000156' 'HsapDv:0000157' 'HsapDv:0000158'\n", + " 'HsapDv:0000159' 'HsapDv:0000160' 'HsapDv:0000162' 'HsapDv:0000163'\n", + " 'HsapDv:0000165' 'HsapDv:0000166' 'HsapDv:0000171' 'HsapDv:0000207'\n", + " 'HsapDv:0000208' 'HsapDv:0000212' 'HsapDv:0000262' 'HsapDv:0000274'] categories {}\n", + "categorical ['surgical resection', 'surgical resection', NaN, 'surgical resection', 'surgical resection', ..., 'surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', NaN]\n", + "Length: 171792\n", + "Categories (1, object): ['surgical resection'] sample_collection_method {}\n", + "array [ 0 0 -1 ... 0 0 -1] codes {}\n", + "string-array ['surgical resection'] categories {}\n", + "categorical ['Baylor College of Medicine Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', NaN, 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', ..., 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', NaN]\n", + "Length: 171792\n", + "Categories (4, object): ['Baylor College of Medicine Lions Eye Bank', 'Massachusetts General Hospital', 'University of Utah', 'Utah Lions Eye Bank, Florida Lions Eye Bank'] tissue_source {}\n", + "array [ 0 3 -1 ... 0 0 -1] codes {}\n", + "string-array ['Baylor College of Medicine Lions Eye Bank'\n", + " 'Massachusetts General Hospital' 'University of Utah'\n", + " 'Utah Lions Eye Bank,\\xa0Florida Lions Eye Bank'] categories {}\n", + "categorical ['tissue', 'tissue', 'tissue', 'tissue', 'tissue', ..., 'tissue', 'tissue', 'tissue', 'tissue', 'tissue']\n", + "Length: 171792\n", + "Categories (1, object): ['tissue'] tissue_type {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['tissue'] categories {}\n", + "categorical ['unknown', 'unknown', NaN, 'unknown', 'unknown', ..., 'unknown', 'unknown', 'unknown', 'unknown', NaN]\n", + "Length: 171792\n", + "Categories (2, object): ['2020', 'unknown'] sample_collection_year {}\n", + "array [ 1 1 -1 ... 1 1 -1] codes {}\n", + "string-array ['2020' 'unknown'] categories {}\n", + "categorical ['mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', ..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat...]\n", + "Length: 171792\n", + "Categories (3, object): ['mechanical dissociation,centrifugation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation'] suspension_derivation_process {}\n", + "array [2 2 1 ... 2 2 1] codes {}\n", + "string-array ['mechanical dissociation,centrifugation'\n", + " 'mechanical dissociation,detergent solubilization'\n", + " 'mechanical dissociation,enzymatic dissociation'] categories {}\n", + "categorical ['8788601b-389e-474c-911c-adedbb3048cc', '3f6daba2-bd69-4df8-a01f-60a8a06b9e83', '3713a0a2-238f-4fcb-b6e3-33a4543d3015', '01b0b422-ea30-4929-bcc2-99465d5107b5', 'af9b61fc-166a-4c27-93c6-d88b65696995', ..., 'c356b586-a9e8-446e-bbc9-78b6b71dd69a', '6d136144-0dcf-41a2-8cc5-fff28f1e4b05', 'c9849ef8-1c97-4655-a36c-7af59fcffcc4', 'd5803a60-248b-4dfc-a8b0-fcc01a5af9c4', '9490337e-9b73-4a52-b76d-bbbeda942c94']\n", + "Length: 171792\n", + "Categories (104, object): ['0bfab131-4aa6-45ba-84a7-53dfb067534d', '0d71495a-c58e-4271-be5f-ed64390d3d0e', '01b0b422-ea30-4929-bcc2-99465d5107b5', '1b8dbc8e-9586-42ba-9125-99664e094f4d', ..., 'ef3f886e-e5dd-41bf-8dfb-701dcd60cbd9', 'ef6e6788-3a53-4208-aedb-13da82d5f1bf', 'f5e609a8-4bdd-421f-92db-479d2d7b1e73', 'fce44b90-bb2b-4daa-b260-961bab432d4c'] suspension_uuid {}\n", + "array [75 14 63 ... 92 94 76] codes {}\n", + "string-array ['0bfab131-4aa6-45ba-84a7-53dfb067534d'\n", + " '0d71495a-c58e-4271-be5f-ed64390d3d0e'\n", + " '01b0b422-ea30-4929-bcc2-99465d5107b5'\n", + " '1b8dbc8e-9586-42ba-9125-99664e094f4d'\n", + " '1b846b54-6cac-4ff5-b9d7-7af799f01528'\n", + " '1bd77e36-d9e4-4f61-bde0-e36249f5f549'\n", + " '2bead1b2-f86e-427c-ac22-db027764e51a'\n", + " '2c24c479-b018-4e6d-a9ab-9ed298593519'\n", + " '2c340a6c-d42d-4f54-9c14-1834f254363b'\n", + " '2c22876d-2c53-4a07-97b9-cc272ddad9af'\n", + " '2dbf1a9a-eb37-4570-af15-56a4f9d5733a'\n", + " '2f91a875-dc06-4225-b143-928c2427ced3'\n", + " '3c219614-c3b9-4f38-91a3-376a0dad898c'\n", + " '3f5db73c-85d8-40c9-97dc-bdf3169f2fd7'\n", + " '3f6daba2-bd69-4df8-a01f-60a8a06b9e83'\n", + " '03fa5208-02f5-4586-b111-bf98d631a97f'\n", + " '4be8fe52-a209-4d8f-8be4-c57f5179af64'\n", + " 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Medicine', ..., 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', NaN]\n", + "Length: 171792\n", + "Categories (2, object): ['Baylor College of Medicine', 'Harvard University'] institute {}\n", + "array [ 0 0 -1 ... 0 0 -1] codes {}\n", + "string-array ['Baylor College of Medicine' 'Harvard University'] categories {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, NaN, NaN, NaN]\n", + "Length: 171792\n", + "Categories (8, object): ['SRX20898918', 'SRX20898919', 'SRX20898920', 'SRX20898921', 'SRX20898922', 'SRX20898923', 'SRX20898924', 'SRX20898925'] library_id_repository {}\n", + "array [-1 -1 -1 ... -1 -1 -1] codes {}\n", + "string-array ['SRX20898918' 'SRX20898919' 'SRX20898920' 'SRX20898921' 'SRX20898922'\n", + " 'SRX20898923' 'SRX20898924' 'SRX20898925'] categories {}\n", + "categorical ['Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', NaN, 'Illumina NovaSeq 6000 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object): ['Adipogenic Progenitors', 'Arterial', 'Arteriole', 'Endothelial Cells', ..., 'Smooth Muscle Cells', 'T/NK/B Cells', 'Vein', 'Venule'] author_cell_type {}\n", + "array [ 5 19 3 ... 20 5 11] codes {}\n", + "string-array ['Adipogenic Progenitors' 'Arterial' 'Arteriole' 'Endothelial Cells'\n", + " 'Erythroblasts - Myelocytes - Mature NK Cells' 'Fenestrated capillary'\n", + " 'Lymphatic Endothelial Cells' 'Lymphoid/B/NK Cells' 'Macrophages'\n", + " 'Mast Cells' 'Mature Adipocytes' 'Mesothelial Cells'\n", + " 'Myeloid Cells (Monocytes, Neutrophils, Macrophages)'\n", + " 'Neuronal-associated Cells' 'PRM1+ Cells' 'Pericytes' 'Schwann Cells'\n", + " 'Smooth Muscle Cells' 'T/NK/B Cells' 'Vein' 'Venule'] categories {}\n", + "categorical ['PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', ..., 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461']\n", + "Length: 171792\n", + "Categories (1, object): ['PATO:0000461'] disease_ontology_term_id {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['PATO:0000461'] categories {}\n", + "categorical ['none', 'none', '[type 2 diabetes mellitus]', 'none', 'none', ..., 'none', 'none', 'none', 'none', 'none']\n", + "Length: 171792\n", + "Categories (3, object): ['['meningeal sarcoma']', '[type 2 diabetes mellitus]', 'none'] reported_diseases {}\n", + "array [2 2 1 ... 2 2 2] codes {}\n", + "string-array [\"['meningeal sarcoma']\" '[type 2 diabetes mellitus]' 'none'] categories {}\n", + "categorical ['PATO:0000384', 'PATO:0000383', 'PATO:0000383', 'PATO:0000383', 'PATO:0000384', ..., 'PATO:0000383', 'PATO:0000384', 'PATO:0000384', 'PATO:0000383', 'PATO:0000383']\n", + "Length: 171792\n", + "Categories (2, object): ['PATO:0000383', 'PATO:0000384'] sex_ontology_term_id {}\n", + "array [1 0 0 ... 1 0 0] codes {}\n", + "string-array ['PATO:0000383' 'PATO:0000384'] categories {}\n", + "array [ 4642. 3048. nan ... 2351. 10119. nan] nCount_RNA {}\n", + 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Post_mortemtime {}\n", + "array [34 14 -1 ... 16 26 -1] codes {}\n", + "string-array ['2h36m' '2h49m' '2h59m' '3h' '3h30m' '3h43m' '3h50m' '3h55m' '4h' '4h9m'\n", + " '4h33m' '4h48m' '5h' '5h11m' '5h18m' '5h40m' '6h' '6h2m' '6h5m' '6h17m'\n", + " '6h28m' '6h30m' '6h+' '7h' '7h26m' '7h31m' '8h' '8h1m' '8h45m' '8h50m'\n", + " '8h55m' '9.5h' '9h' '9h10m' '10h' 'Unknown'] categories {}\n", + "categorical ['10', '5.3', NaN, '9.5', '9', ..., '6.5', '10', '6', '8', NaN]\n", + "Length: 171792\n", + "Categories (36, object): ['2.6', '2.82', '2.98', '3', ..., '9.17', '10', '>6', 'Unknown'] PMT_in_hrs {}\n", + "array [33 13 -1 ... 16 25 -1] codes {}\n", + "string-array ['2.6' '2.82' '2.98' '3' '3.5' '3.72' '3.83' '3.92' '4' '4.8' '4.15'\n", + " '4.55' '5' '5.3' '5.18' '5.67' '6' '6.03' '6.5' '6.08' '6.28' '6.47' '7'\n", + " '7.43' '7.52' '8' '8.02' '8.75' '8.83' '8.92' '9' '9.5' '9.17' '10' '>6'\n", + " 'Unknown'] categories {}\n", + "categorical ['Unknown', 'OS', NaN, 'Unknown', 'Unknown', ..., 'OD', 'Unknown', 'Unknown', 'Unknown', NaN]\n", + "Length: 171792\n", + "Categories (3, object): ['OD', 'OS', 'Unknown'] Eye {}\n", + "array [ 2 1 -1 ... 2 2 -1] codes {}\n", + "string-array ['OD' 'OS' 'Unknown'] categories {}\n", + "categorical ['Peripheral', 'Peripheral', NaN, 'Macular', 'Peripheral', ..., 'Macular', 'Macular', 'Peripheral', 'Peripheral', NaN]\n", + "Length: 171792\n", + "Categories (2, object): ['Macular', 'Peripheral'] Region {}\n", + "array [ 1 1 -1 ... 1 1 -1] codes {}\n", + "string-array ['Macular' 'Peripheral'] categories {}\n", + "categorical ['3v31_BCM_1d_fetal_RPE', '3v31_MMD_23_2292_RPE', NaN, '3v31_BCM_23-1430_Mac_RPE', '3v31_BCM_22_0890_RPE', ..., '3v31_MMD_23-4291_Mac_RPE', '3v31_BCM_22-0698_Mac_RPE', '3v31_BCM_23_0313_RPE', '3v31_BCM_22_0458_RPE', NaN]\n", + "Length: 171792\n", + "Categories (82, object): ['3v31_22_0574_RPE', '3v31_22_0574_RPE_Tyto', '3v31_BCM_1d_fetal_RPE', '3v31_BCM_22-0396_Mac_RPE', ..., 'GSM7553466', 'GSM7553467', 'GSM7553469', 'GSM7553471'] sampleid {}\n", + "array [ 2 64 -1 ... 32 16 -1] codes {}\n", + "string-array ['3v31_22_0574_RPE' '3v31_22_0574_RPE_Tyto' '3v31_BCM_1d_fetal_RPE'\n", + " '3v31_BCM_22-0396_Mac_RPE' '3v31_BCM_22-0434_Mac_RPE'\n", + " '3v31_BCM_22-0698_Mac_RPE' '3v31_BCM_22-0769_Mac_RPE'\n", + " '3v31_BCM_22-0849_Mac_RPE' '3v31_BCM_22_0183_Mac_RPE'\n", + " '3v31_BCM_22_0183_RPE_WOLF' '3v31_BCM_22_0200_Mac_RPE'\n", + " '3v31_BCM_22_0200_RPE' '3v31_BCM_22_0389_RPE' '3v31_BCM_22_0396_RPE_WOLF'\n", + " '3v31_BCM_22_0434_RPE' '3v31_BCM_22_0434_RPE_WOLF' '3v31_BCM_22_0458_RPE'\n", + " '3v31_BCM_22_0500_RPE' '3v31_BCM_22_0769_RPE_WOLF'\n", + " '3v31_BCM_22_0784_Mac_RPE' '3v31_BCM_22_0784_RPE_WOLF'\n", + " '3v31_BCM_22_0849_RPE' '3v31_BCM_22_0890_RPE' '3v31_BCM_22_0896_RPE_WOLF'\n", + " '3v31_BCM_23-0131_Mac_RPE' '3v31_BCM_23-0231_Mac_RPE'\n", + " '3v31_BCM_23-0334_Mac_RPE' '3v31_BCM_23-1401_Mac_RPE'\n", + " '3v31_BCM_23-1430_Mac_RPE' '3v31_BCM_23-1448_Mac_RPE'\n", + " '3v31_BCM_23_0131_RPE' '3v31_BCM_23_0231_RPE' '3v31_BCM_23_0313_RPE'\n", + " '3v31_BCM_23_0334_RPE' '3v31_BCM_23_0358_RPE' '3v31_BCM_23_0491_RPE'\n", + " '3v31_MMD_19_D005_Mac_RPE' '3v31_MMD_19_D005_RPE'\n", + " '3v31_MMD_19_D008_Mac_RPE' '3v31_MMD_19_D008_RPE'\n", + " '3v31_MMD_22-3051_Mac_RPE' '3v31_MMD_22-3131_Mac_RPE'\n", + " '3v31_MMD_22-3991_Mac_RPE' '3v31_MMD_22-7151_Mac_RPE'\n", + " '3v31_MMD_22_1972_RPE' '3v31_MMD_22_2854_RPE' '3v31_MMD_22_3053_RPE'\n", + " '3v31_MMD_22_3132_RPE' '3v31_MMD_22_3872_RPE' '3v31_MMD_22_3952_RPE_1'\n", + " '3v31_MMD_22_3952_RPE_2' '3v31_MMD_22_3992_RPE' '3v31_MMD_22_4472_RPE'\n", + " '3v31_MMD_22_5352_RPE' '3v31_MMD_22_6392_RPE' '3v31_MMD_22_6432_RPE'\n", + " '3v31_MMD_22_7032_RPE' '3v31_MMD_22_7072_RPE' '3v31_MMD_22_7152_RPE'\n", + " '3v31_MMD_22_7432_RPE' '3v31_MMD_23-4291_Mac_RPE' '3v31_MMD_23_0194_RPE'\n", + " '3v31_MMD_23_334_RPE' '3v31_MMD_23_2252_RPE' '3v31_MMD_23_2292_RPE'\n", + " '3v31_MMD_23_3312_RPE' '3v31_MMD_23_4292_RPE' '3v31_MMD_23_5453_RPE'\n", + " '5v2_22_2854_per_RPE' '5v2_22_2854_per_RPE_spin' '10x3V31_22_0183_RPE_1'\n", + " '10x3V31_22_0183_RPE_2' '10x3V31_Adult_20_0948_Lobe_RPE'\n", + " '22_4472_per_RPE_Nu' 'GSM7553460' 'GSM7553461' 'GSM7553463' 'GSM7553464'\n", + " 'GSM7553466' 'GSM7553467' 'GSM7553469' 'GSM7553471'] categories {}\n", + "categorical ['fenestrated endothelial cell', 'vein endothelial cell', 'endothelial cell', 'endothelial cell of venule', 'fenestrated endothelial cell', ..., 'endothelial cell of artery', 'endothelial cell of venule', 'endothelial cell of venule', 'fenestrated endothelial cell', 'mesothelial cell']\n", + "Length: 171792\n", + "Categories (20, object): ['Schwann cell', 'adipocyte', 'endothelial cell', 'endothelial cell of arteriole', ..., 'pericyte', 'smooth muscle cell', 'unknown', 'vein endothelial cell'] cell_type {}\n", + "array [ 7 19 2 ... 6 7 13] codes {}\n", + "string-array ['Schwann cell' 'adipocyte' 'endothelial cell'\n", + " 'endothelial cell of arteriole' 'endothelial cell of artery'\n", + " 'endothelial cell of lymphatic vessel' 'endothelial cell of venule'\n", + " 'fenestrated endothelial cell' 'fibro/adipogenic progenitor cell'\n", + " 'hematopoietic cell' 'lymphocyte' 'macrophage' 'mast cell'\n", + " 'mesothelial cell' 'myeloid cell' 'neuron associated cell' 'pericyte'\n", + " 'smooth muscle cell' 'unknown' 'vein endothelial cell'] categories {}\n", + "categorical ['10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', ..., '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3']\n", + "Length: 171792\n", + "Categories (2, object): ['10x 5' v2', '10x 3' v3'] assay {}\n", + "array [1 1 1 ... 1 1 1] codes {}\n", + "string-array [\"10x 5' v2\" \"10x 3' v3\"] categories {}\n", + "categorical ['normal', 'normal', 'normal', 'normal', 'normal', ..., 'normal', 'normal', 'normal', 'normal', 'normal']\n", + "Length: 171792\n", + "Categories (1, object): ['normal'] disease {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['normal'] categories {}\n", + "categorical ['male', 'female', 'female', 'female', 'male', ..., 'female', 'male', 'male', 'female', 'female']\n", + "Length: 171792\n", + "Categories (2, object): ['female', 'male'] sex {}\n", + "array [1 0 0 ... 1 0 0] codes {}\n", + "string-array ['female' 'male'] categories {}\n", + "categorical ['chorioretinal region', 'chorioretinal region', 'visceral abdominal adipose tissue', 'chorioretinal region', 'chorioretinal region', ..., 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'visceral abdominal adipose tissue']\n", + "Length: 171792\n", + "Categories (3, object): ['chorioretinal region', 'subcutaneous abdominal adipose tissue', 'visceral abdominal adipose tissue'] tissue {}\n", + "array [0 0 2 ... 0 0 2] codes {}\n", + "string-array ['chorioretinal region' 'subcutaneous abdominal adipose tissue'\n", + " 'visceral abdominal adipose tissue'] categories {}\n", + "categorical ['European', 'African American', 'European', 'African American', 'Indian', ..., 'African American', 'European', 'European', 'Hispanic or Latin American', 'African American']\n", + "Length: 171792\n", + "Categories (6, object): ['European', 'South Asian', 'Hispanic or Latin American', 'Indian', 'African American', 'unknown'] self_reported_ethnicity {}\n", + "array [0 4 0 ... 0 2 4] codes {}\n", + "string-array ['European' 'South Asian' 'Hispanic or Latin American' 'Indian'\n", + " 'African American' 'unknown'] categories {}\n", + "categorical ['newborn stage (0-28 days)', '60-year-old stage', '66-year-old stage', '90 year-old and over stage', '64-year-old stage', ..., '10-year-old stage', 'newborn stage (0-28 days)', '60-year-old stage', '25-year-old stage', '35-year-old stage']\n", + "Length: 171792\n", + "Categories (40, object): ['10-year-old stage', '11-year-old stage', '16-year-old stage', '17-year-old stage', ..., '82-year-old stage', '86-year-old stage', '90 year-old and over stage', 'newborn stage (0-28 days)'] development_stage {}\n", + "array [39 24 29 ... 24 6 13] codes {}\n", + "string-array ['10-year-old stage' '11-year-old stage' '16-year-old stage'\n", + " '17-year-old stage' '18-year-old stage' '21-year-old stage'\n", + " '25-year-old stage' '26-year-old stage' '27-year-old stage'\n", + " '28-year-old stage' '30-year-old stage' '32-year-old stage'\n", + " '34-year-old stage' '35-year-old stage' '37-year-old stage'\n", + " '41-year-old stage' '43-year-old stage' '46-year-old stage'\n", + " '47-year-old stage' '50-year-old stage' '51-year-old stage'\n", + " '53-year-old stage' '54-year-old stage' '58-year-old stage'\n", + " '60-year-old stage' '62-year-old stage' '63-year-old stage'\n", + " '64-year-old stage' '65-year-old stage' '66-year-old stage'\n", + " '68-year-old stage' '69-year-old stage' '71-year-old stage'\n", + " '72-year-old stage' '77-year-old stage' '81-year-old stage'\n", + " '82-year-old stage' '86-year-old stage' '90 year-old and over stage'\n", + " 'newborn stage (0-28 days)'] categories {}\n", + "string-array ['7jCOp<6|em' ';, 'X_umap': dask.array} obsm {}\n", + "array dask.array X_scVI {'shards': (171008, 100), 'chunks': (1024, 100), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "array dask.array X_umap {'shards': (171008, 2), 'chunks': (1024, 2), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "dict {} varm {}\n", + "dict {} obsp {}\n", + "dict {} varp {}\n", + "dict {} layers {}\n", + "dict {} uns {}\n", + "raw Raw AnnData with n_obs × n_vars = 171792 × 36406 raw {}\n", + "csr_matrix dask.array X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "csr_matrix \n", + " Coords\tValues\n", + " (0, 6381)\t0.0\n", + " (0, 7766)\t0.0\n", + " (0, 8748)\t0.0\n", + " (0, 8975)\t0.0\n", + " (0, 12475)\t0.0\n", + " (0, 12479)\t0.0\n", + " (0, 12481)\t0.0\n", + " (0, 13841)\t0.0\n", + " (0, 14274)\t0.0\n", + " (0, 14909)\t0.0\n", + " (0, 16128)\t0.0\n", + " (0, 17261)\t0.0\n", + " (0, 17271)\t0.0\n", + " (0, 17497)\t0.0\n", + " (0, 17896)\t0.0\n", + " (0, 18254)\t0.0\n", + " (0, 18515)\t0.0\n", + " (0, 18518)\t0.0\n", + " (0, 18532)\t0.0\n", + " (0, 18743)\t0.0\n", + " (0, 18745)\t0.0\n", + " (0, 18769)\t0.0\n", + " (0, 18790)\t0.0\n", + " (0, 18794)\t0.0\n", + " (0, 18807)\t0.0\n", + " :\t:\n", + " (986, 36077)\t0.0\n", + " (986, 36088)\t0.0\n", + " (986, 36101)\t0.0\n", + " (986, 36114)\t0.0\n", + " (986, 36120)\t0.0\n", + " (986, 36133)\t0.0\n", + " (986, 36140)\t0.0\n", + " (986, 36143)\t0.0\n", + " (986, 36149)\t0.0\n", + " (986, 36158)\t0.0\n", + " (986, 36179)\t0.0\n", + " (986, 36211)\t0.0\n", + " (986, 36214)\t0.0\n", + " (986, 36224)\t0.0\n", + " (986, 36244)\t0.0\n", + " (986, 36269)\t0.0\n", + " (986, 36285)\t0.0\n", + " (986, 36310)\t0.0\n", + " (986, 36318)\t0.0\n", + " (986, 36363)\t0.0\n", + " (986, 36373)\t0.0\n", + " (986, 35974)\t1.0\n", + " (986, 36296)\t1.0\n", + " (986, 36393)\t2.0\n", + " (986, 36075)\t1.0 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ubuntu/home_drive/volume/arrayloaders/venv/lib/python3.12/site-packages/zarr/api/asynchronous.py:244: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.\n", + " warnings.warn(\n", + "100%|██████████| 1/1 [11:12<00:00, 672.25s/it]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dataframe Empty DataFrame\n", + "Columns: []\n", + "Index: [ENSG00000000003, ENSG00000000005, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000000938, ENSG00000000971, ENSG00000001036, ENSG00000001084, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001561, ENSG00000001617, ENSG00000001626, ENSG00000001629, ENSG00000001630, ENSG00000001631, ENSG00000002016, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002726, ENSG00000002745, ENSG00000002746, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000002933, ENSG00000003056, ENSG00000003096, ENSG00000003137, ENSG00000003147, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003756, ENSG00000003987, ENSG00000003989, ENSG00000004059, ENSG00000004139, ENSG00000004142, ENSG00000004399, ENSG00000004455, ENSG00000004468, ENSG00000004478, ENSG00000004487, ENSG00000004534, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004776, ENSG00000004777, ENSG00000004779, ENSG00000004799, ENSG00000004809, ENSG00000004838, ENSG00000004846, ENSG00000004848, ENSG00000004864, ENSG00000004866, ENSG00000004897, ENSG00000004939, ENSG00000004948, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG00000005100, ENSG00000005102, ENSG00000005108, ENSG00000005156, ENSG00000005175, ENSG00000005187, ENSG00000005189, ENSG00000005194, ENSG00000005206, ENSG00000005238, ENSG00000005243, ENSG00000005249, ENSG00000005302, ENSG00000005339, ENSG00000005379, ENSG00000005381, ENSG00000005421, ENSG00000005436, ENSG00000005448, ENSG00000005469, ENSG00000005471, ENSG00000005483, ...]\n", + "\n", + "[36406 rows x 0 columns] var {}\n", + "string-array ['ENSG00000000003' 'ENSG00000000005' 'ENSG00000000419' ...\n", + " 'ENSG00000289604' 'ENSG00000290292' 'ENSG00000291237'] _index {}\n", + "dict {} varm {}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + } + ], "source": [ "from annbatch import create_anndata_collection\n", + "from anndata import AnnData\n", + "\n", + "def del_layers(adata: AnnData) -> AnnData:\n", + " del adata.layers # soupX is present in one of the datasets' layers but not the other\n", + " return adata\n", "\n", "create_anndata_collection(\n", " # List all the h5ad files you want to include in the collection\n", @@ -105,6 +1274,7 @@ " n_obs_per_dataset=2_097_152, # Number of cells per dataset shard\n", " var_subset=None, # Optionally subset the collection to a specific gene space\n", " should_denseify=False,\n", + " transform_input_adata=del_layers\n", ")" ] }, @@ -117,7 +1287,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -128,9 +1298,20 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "import anndata as ad\n", "\n", @@ -141,6 +1322,7 @@ " chunk_size=256, # Number of obs to load from disk contiguously - default settings should work well\n", " preload_nchunks=32, # Number of chunks to preload + shuffle - default settings should work well\n", " preload_to_gpu=False, # If True, preloaded chunks are moved to GPU memory via `cupy`, which can put more pressure on GPU memory but will accelerate loading ~20%\n", + " to_torch=True\n", ")\n", "\n", "# Add dataset that should be used for training\n", @@ -170,12 +1352,24 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 13, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + " 0%| | 0/171792 [00:00\n", + " Coords\tValues\n", + " (0, 6381)\t0.0\n", + " (0, 7766)\t0.0\n", + " (0, 8748)\t0.0\n", + " (0, 8975)\t0.0\n", + " (0, 12475)\t0.0\n", + " (0, 12479)\t0.0\n", + " (0, 12481)\t0.0\n", + " (0, 13841)\t0.0\n", + " (0, 14274)\t0.0\n", + " (0, 14909)\t0.0\n", + " (0, 16128)\t0.0\n", + " (0, 17261)\t0.0\n", + " (0, 17271)\t0.0\n", + " (0, 17497)\t0.0\n", + " (0, 17896)\t0.0\n", + " (0, 18254)\t0.0\n", + " (0, 18515)\t0.0\n", + " (0, 18518)\t0.0\n", + " (0, 18532)\t0.0\n", + " (0, 18743)\t0.0\n", + " (0, 18745)\t0.0\n", + " (0, 18769)\t0.0\n", + " (0, 18790)\t0.0\n", + " (0, 18794)\t0.0\n", + " (0, 18807)\t0.0\n", + " :\t:\n", + " (271248, 14024)\t3.7011654376983643\n", + " (271248, 4718)\t2.8212473392486572\n", + " (271248, 15390)\t2.8212473392486572\n", + " (271248, 4666)\t2.185926914215088\n", + " (271248, 1878)\t2.185926914215088\n", + " (271248, 5874)\t3.2066688537597656\n", + " (271248, 714)\t2.185926914215088\n", + " (271248, 8744)\t2.185926914215088\n", + " (271248, 4540)\t2.8212473392486572\n", + " (271248, 10607)\t2.185926914215088\n", + " (271248, 4525)\t2.185926914215088\n", + " (271248, 15093)\t2.185926914215088\n", + " (271248, 12417)\t2.185926914215088\n", + " (271248, 6650)\t2.185926914215088\n", + " (271248, 16129)\t2.185926914215088\n", + " (271248, 16297)\t2.185926914215088\n", + " (271248, 8169)\t2.8212473392486572\n", + " (271248, 5696)\t2.185926914215088\n", + " (271248, 8185)\t2.185926914215088\n", + " (271248, 10613)\t2.185926914215088\n", + " (271248, 10141)\t2.185926914215088\n", + " (271248, 642)\t2.185926914215088\n", + " (271248, 17141)\t2.185926914215088\n", + " (271248, 8153)\t3.4841766357421875\n", + " (271248, 4520)\t2.8212473392486572 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "dataframe reference_genome \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 GRCh38 \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 GRCh38 \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 GRCh38 \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 GRCh38 \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 GRCh38 \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 GRCh38 \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 GRCh38 \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 GRCh38 \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 GRCh38 \n", + "\n", + " gene_annotation_version \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 v98 \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 v98 \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 v98 \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 v98 \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 v98 \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 v98 \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 v98 \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 v98 \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 v98 \n", + "\n", + " alignment_software \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 Cell Ranger count v7.1.0 \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 Cell Ranger count v7.1.0 \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 Cell Ranger count v7.1.0 \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 Cell Ranger count v7.1.0 \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 Cell Ranger count v7.1.0 \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 Cell Ranger count v7.1.0 \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 Cell Ranger count v7.1.0 \n", + "\n", + " intronic_reads_counted \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 yes \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 yes \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 yes \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 yes \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 yes \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 yes \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 yes \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 yes \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 yes \n", + "\n", + " donor_id donor_age \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 MMD_23_17738 10 years \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 MMD_22_20372 65 years \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 MMD_23_17738 10 years \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 BCM_22_0183 21 years \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 BCM_22_0698 1 day \n", + "... ... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 BCM_23_0491 16 years \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 BCM_22_0500 64 years \n", + "CGTAATGCAGCCGGTT-1-BOM donor-BLUE NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 MMD_22_17939 71 years \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 MMD_22_38029 82 years \n", + "\n", + " self_reported_ethnicity_ontology_term_id \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 HANCESTRO:0568 \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 HANCESTRO:0568 \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 HANCESTRO:0568 \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 HANCESTRO:0005 \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 HANCESTRO:0005 \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 HANCESTRO:0568 \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 HANCESTRO:0005 \n", + "CGTAATGCAGCCGGTT-1-BOM HANCESTRO:0568 \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 HANCESTRO:0568 \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 HANCESTRO:0014 \n", + "\n", + " donor_cause_of_death \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 unknown \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 unknown \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 unknown \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 unknown \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 unknown \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 unknown \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 unknown \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 unknown \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 unknown \n", + "\n", + " donor_living_at_sample_collection \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 False \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 False \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 False \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 False \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 False \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 False \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 False \n", + "CGTAATGCAGCCGGTT-1-BOM True \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 False \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 False \n", + "\n", + " sample_id \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 67d22e15-0d05-4c65-bda4-9cb350949266 \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 4722f3bd-2909-4026-b0b9-c471f4455658 \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 27848b53-eddb-44d6-894f-070488287fc2 \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 16565f49-122b-4ae2-93b2-c772d76fa697 \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 e322b3ae-fdee-462a-a4b3-37009212d7ed \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 46737bca-3ca2-451d-96fb-ebb433159f41 \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 8e799a46-d8e2-4e72-a483-414168d778b5 \n", + "CGTAATGCAGCCGGTT-1-BOM NaN \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 55c1fb02-40ca-462c-8578-9196e3c83f89 \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 dbe62368-43f4-41ed-a2e7-7d696b5f19d2 \n", + "\n", + " ... mapped_reference_annotation \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 ... NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 ... NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 ... NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 ... NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 ... NaN \n", + "... ... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 ... NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 ... NaN \n", + "CGTAATGCAGCCGGTT-1-BOM ... GENCODE 32 \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 ... NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 ... NaN \n", + "\n", + " sample_uuid \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM c3516e93-6857-4fb2-8eab-31038dbab88d \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " sample_derivation_process \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM dissection \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " sample_source \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM Brigham and Women's Hospital \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " donor_BMI_at_collection \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM 42.93 \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " suspension_dissociation_reagent \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM Cytoplasmic cell lysis buffer \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " suspension_dissociation_time \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM 20 minute \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " library_uuid \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM 158fa263-4d48-4894-96e2-69eba15c4c5f \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " library_starting_quantity \\\n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM 10000 nuclei \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + " leiden_scVI \n", + "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", + "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", + "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", + "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", + "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", + "... ... \n", + "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", + "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", + "CGTAATGCAGCCGGTT-1-BOM 7 \n", + "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", + "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", + "\n", + "[271249 rows x 61 columns] obs {}\n", + "string-array ['3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1'\n", + " '3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1'\n", + " '3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1' ...\n", + " 'CGTAATGCAGCCGGTT-1-BOM' '3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1'\n", + " '3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1'] _index {}\n", + "categorical ['GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', ..., 'GRCh38', 'GRCh38', NaN, 'GRCh38', 'GRCh38']\n", + "Length: 271249\n", + "Categories (1, object): ['GRCh38'] reference_genome {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['GRCh38'] categories {}\n", + "categorical ['v98', 'v98', 'v98', 'v98', 'v98', ..., 'v98', 'v98', NaN, 'v98', 'v98']\n", + "Length: 271249\n", + "Categories (1, object): ['v98'] gene_annotation_version {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['v98'] categories {}\n", + "categorical ['Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', ..., 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN, 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0']\n", + "Length: 271249\n", + "Categories (2, object): ['Cell Ranger count v7.0.1', 'Cell Ranger count v7.1.0'] alignment_software {}\n", + "array [ 1 1 1 ... -1 1 1] codes {}\n", + "string-array ['Cell Ranger count v7.0.1' 'Cell Ranger count v7.1.0'] categories {}\n", + "categorical ['yes', 'yes', 'yes', 'yes', 'yes', ..., 'yes', 'yes', NaN, 'yes', 'yes']\n", + "Length: 271249\n", + "Categories (1, object): ['yes'] intronic_reads_counted {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['yes'] categories {}\n", + "categorical ['MMD_23_17738', 'MMD_22_20372', 'MMD_23_17738', 'BCM_22_0183', 'BCM_22_0698', ..., 'BCM_23_0491', 'BCM_22_0500', 'donor-BLUE', 'MMD_22_17939', 'MMD_22_38029']\n", + "Length: 271249\n", + "Categories (71, object): ['BCM_21_0948', 'BCM_22_0183', 'BCM_22_0200', 'BCM_22_0396', ..., 'donor-SILK', 'donor-TIME', 'donor-TREE', 'donor-ZONE'] donor_id {}\n", + "array [50 39 50 ... 53 36 46] codes {}\n", + "string-array ['BCM_21_0948' 'BCM_22_0183' 'BCM_22_0200' 'BCM_22_0396' 'BCM_22_0434'\n", + " 'BCM_22_0458' 'BCM_22_0500' 'BCM_22_0698' 'BCM_22_0769' 'BCM_22_0784'\n", + " 'BCM_22_0849' 'BCM_22_0890' 'BCM_22_0896' 'BCM_23_0131' 'BCM_23_0231'\n", + " 'BCM_23_0313' 'BCM_23_0334' 'BCM_23_0358' 'BCM_23_0491' 'BCM_23_0574'\n", + " 'BCM_23_1401' 'BCM_23_1430' 'BCM_23_1448' 'Hu13' 'Hu0218' 'Hu0220'\n", + " 'Hu0222' 'Hu0235' 'MMD_19_D005' 'MMD_19_D008' 'MMD_22_13066'\n", + " 'MMD_22_14307' 'MMD_22_16608' 'MMD_22_16860' 'MMD_22_17017'\n", + " 'MMD_22_17464' 'MMD_22_17939' 'MMD_22_20137' 'MMD_22_20357'\n", + " 'MMD_22_20372' 'MMD_22_21878' 'MMD_22_25357' 'MMD_22_33472'\n", + " 'MMD_22_34032' 'MMD_22_37089' 'MMD_22_37117' 'MMD_22_38029'\n", + " 'MMD_22_38453' 'MMD_23_01524' 'MMD_23_02177' 'MMD_23_17738'\n", + " 'MMD_23_21999' 'donor-APEX' 'donor-BLUE' 'donor-BOAT' 'donor-CORK'\n", + " 'donor-COST' 'donor-DOVE' 'donor-DOWN' 'donor-GOLD' 'donor-KEYS'\n", + " 'donor-KISS' 'donor-LACE' 'donor-OATS' 'donor-PASS' 'donor-PIKE'\n", + " 'donor-PINK' 'donor-SILK' 'donor-TIME' 'donor-TREE' 'donor-ZONE'] categories {}\n", + "categorical ['10 years', '65 years', '10 years', '21 years', '1 day', ..., '16 years', '64 years', NaN, '71 years', '82 years']\n", + "Length: 271249\n", + "Categories (31, object): ['1 day', '10 years', '11 years', '16 years', ..., '81 years', '82 years', '86 years', '>89 years'] donor_age {}\n", + "array [ 1 21 1 ... -1 24 28] codes {}\n", + "string-array ['1 day' '10 years' '11 years' '16 years' '17 years' '21 years' '25 years'\n", + " '27 years' '30 years' '32 years' '34 years' '43 years' '46 years'\n", + " '47 years' '50 years' '53 years' '58 years' '60 years' '62 years'\n", + " '63 years' '64 years' '65 years' '68 years' '69 years' '71 years'\n", + " '72 years' '77 years' '81 years' '82 years' '86 years' '>89 years'] categories {}\n", + "categorical ['HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0005', ..., 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0014']\n", + "Length: 271249\n", + "Categories (6, object): ['HANCESTRO:0005', 'HANCESTRO:0006', 'HANCESTRO:0014', 'HANCESTRO:0487', 'HANCESTRO:0568', 'unknown'] self_reported_ethnicity_ontology_term_id {}\n", + "array [4 4 4 ... 4 4 2] codes {}\n", + "string-array ['HANCESTRO:0005' 'HANCESTRO:0006' 'HANCESTRO:0014' 'HANCESTRO:0487'\n", + " 'HANCESTRO:0568' 'unknown'] categories {}\n", + "categorical ['unknown', 'unknown', 'unknown', 'unknown', 'unknown', ..., 'unknown', 'unknown', NaN, 'unknown', 'unknown']\n", + "Length: 271249\n", + "Categories (5, object): ['Coronary Artery Disease', 'Malignant Neoplasm', 'Meningeal Sarcoma', 'Septicemia', 'unknown'] donor_cause_of_death {}\n", + "array [ 4 4 4 ... -1 4 4] codes {}\n", + "string-array ['Coronary Artery Disease' 'Malignant Neoplasm' 'Meningeal Sarcoma'\n", + " 'Septicemia' 'unknown'] categories {}\n", + "categorical ['False', 'False', 'False', 'False', 'False', ..., 'False', 'False', 'True', 'False', 'False']\n", + "Length: 271249\n", + "Categories (2, object): ['False', 'True'] donor_living_at_sample_collection {}\n", + "array [0 0 0 ... 1 0 0] codes {}\n", + "string-array ['False' 'True'] categories {}\n", + "categorical ['67d22e15-0d05-4c65-bda4-9cb350949266', '4722f3bd-2909-4026-b0b9-c471f4455658', '27848b53-eddb-44d6-894f-070488287fc2', '16565f49-122b-4ae2-93b2-c772d76fa697', 'e322b3ae-fdee-462a-a4b3-37009212d7ed', ..., '46737bca-3ca2-451d-96fb-ebb433159f41', '8e799a46-d8e2-4e72-a483-414168d778b5', NaN, '55c1fb02-40ca-462c-8578-9196e3c83f89', 'dbe62368-43f4-41ed-a2e7-7d696b5f19d2']\n", + "Length: 271249\n", + "Categories (74, object): ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49', '01ffac9d-c058-47a0-969a-cb8fb51ffd03', '02be6452-fe86-4589-84a2-cbb26954a76f', '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce', ..., 'ed6fd53b-c1c3-49db-b1bb-112362a63b08', 'f86e512c-166d-41fc-b41c-b7baf70709a5', 'f768fecc-f180-420c-9b86-672ad0233e18', 'f932e7b5-1e6e-435d-8ad0-f340287da943'] sample_id {}\n", + "array [19 30 33 ... -1 17 65] codes {}\n", + "string-array ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49'\n", + " '01ffac9d-c058-47a0-969a-cb8fb51ffd03'\n", + " '02be6452-fe86-4589-84a2-cbb26954a76f'\n", + " '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce'\n", + " '5a2a6a3c-8f15-4eab-b2d1-7a6082659a83'\n", + " '5ae43655-e166-4c87-a0fd-13ee2eb525fc'\n", + " '5b839bc9-40f6-4b83-a039-2c424c917971'\n", + " '6a0b4dbd-5147-40ea-998a-3d578ae97d11'\n", + " '6fa3060a-d2b5-4cef-893f-f0b1f523ecc1'\n", + " '8e799a46-d8e2-4e72-a483-414168d778b5'\n", + " '9bc800be-b52f-485e-935b-b5bdda9fc5b8'\n", + " '12b49488-2f2d-4626-bffa-94aee3877981'\n", + " '24d12edd-fd54-4f44-9d21-63ee3c6fc807'\n", + " '25cc7497-b4b6-40e4-88ef-c0a2fe56a3ad'\n", + " '26bf8386-4a13-4fbc-8ff3-e85230a443a3'\n", + " '51e6ba30-757c-4c86-8492-16844de41645'\n", + " '54eb2056-e459-4edb-8bc8-d6adba201d61'\n", + " '55c1fb02-40ca-462c-8578-9196e3c83f89'\n", + " '64fff8e1-8db7-42e4-85df-b76ab1727414'\n", + " '67d22e15-0d05-4c65-bda4-9cb350949266'\n", + " '70df48a7-3d69-46e7-bacd-cdebc9bb6298'\n", + " '87ce0e14-0df9-4d53-99ba-9f1ebca7de9f'\n", + " '90b737c6-9ac7-4f8c-9efc-465a67874a63'\n", + " '136c4a3b-4502-4e7b-8851-fe332faf844c'\n", + " '242cabad-f81d-4fd7-8df7-fe0b318b6c34'\n", + " '245f8d19-2496-4fc0-953c-e202e74397a7'\n", + " '356c1cec-5dfc-4ed4-b07d-2f4b09dbc260'\n", + " '616d8f67-6128-4f7a-b2b3-8205f3d7d72d'\n", + " '654adbbe-18f1-42ea-944b-8aa5f5848567'\n", + " '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7'\n", + " '4722f3bd-2909-4026-b0b9-c471f4455658'\n", + " '9383cb3d-f39c-48c7-b0d6-6cfc26307523'\n", + " '16565f49-122b-4ae2-93b2-c772d76fa697'\n", + " '27848b53-eddb-44d6-894f-070488287fc2'\n", + " '46737bca-3ca2-451d-96fb-ebb433159f41'\n", + " '47201e9a-732d-4bfa-9279-2dea84738e2b'\n", + " '71357c06-8ba6-4b26-bd1a-531c84a9c589'\n", + " '91523cbf-a9f1-4451-8dec-53528db17ca0'\n", + " '632242f1-c6e3-4e8e-926e-c4973fd4e695'\n", + " '717599fd-3926-428e-be6a-a959904b7c1a'\n", + " '994416c8-9bc5-4c1c-9d7c-379d4b53b573'\n", + " '4826577c-c1a3-4c38-bb75-fdce5e6bec62'\n", + " '5586185c-a422-4441-a069-8bc8c652a347'\n", + " '76993467-f2ba-47ff-a967-fa5fbd373f81'\n", + " 'a2b49712-d112-443c-b144-51bf0c54875e'\n", + " 'a9df5458-8c11-4e0b-a3a5-aea273628f77'\n", + " 'a77bec3b-125a-4e1e-9559-739a1adb2e6b'\n", + " 'a89c72dd-c1bf-4029-95d1-b536fb1d71fc'\n", + " 'a3221835-bb93-41c7-a346-2e865b7ab0f4'\n", + " 'ac44c485-ca45-4d66-97fe-6e57b5f2d596'\n", + " 'ae8cde23-b13a-4d9c-80c3-7ea83ee3c9c1'\n", + " 'b0f3f8b7-7f1e-4f5b-95e1-bffc6768706e'\n", + " 'b1dfa534-8408-4be9-99ff-7786f212ea85'\n", + " 'b9ff532d-9b1e-4db9-a69b-546881161bc9'\n", + " 'b30f2bdb-b49e-4464-aa85-046405e04b64'\n", + " 'c5d8d707-3bac-48ce-b65c-224eb5fd452d'\n", + " 'c41fee38-b774-414d-808d-2264e9e008f8'\n", + " 'c46e21e1-edd7-4375-a3a7-c572b3049643'\n", + " 'c934ed75-6076-461d-90ad-03cb05722656'\n", + " 'c48684a8-64af-4cfd-b27f-bcdb57a7b50e'\n", + " 'cb51c83e-0e40-40c7-992a-d08aa2f723b7'\n", + " 'cea8e120-51db-44d0-833a-3745263db2ed'\n", + " 'cf31224c-d03a-4d8a-bdef-6ea449f2d5bf'\n", + " 'd764bae0-929a-4c88-ab6b-671050059c32'\n", + " 'd5182d45-c110-4fae-bed0-58d1a6208820'\n", + " 'dbe62368-43f4-41ed-a2e7-7d696b5f19d2'\n", + " 'dcdbb48e-575b-436d-a3bf-271d2625bb64'\n", + " 'dd9809d7-f120-46e6-af75-d6cdb93115ea'\n", + " 'e322b3ae-fdee-462a-a4b3-37009212d7ed'\n", + " 'e696ec77-06d7-4e17-83fa-2d97499b7e68'\n", + " 'ed6fd53b-c1c3-49db-b1bb-112362a63b08'\n", + " 'f86e512c-166d-41fc-b41c-b7baf70709a5'\n", + " 'f768fecc-f180-420c-9b86-672ad0233e18'\n", + " 'f932e7b5-1e6e-435d-8ad0-f340287da943'] categories {}\n", + "categorical ['frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', ..., 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen']\n", + "Length: 271249\n", + "Categories (2, object): ['flash-freezing', 'frozen in liquid nitrogen'] sample_preservation_method {}\n", + "array [1 1 1 ... 0 1 1] codes {}\n", + "string-array ['flash-freezing' 'frozen in liquid nitrogen'] categories {}\n", + "categorical ['UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', ..., 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0014455', 'UBERON:0019207', 'UBERON:0019207']\n", + "Length: 271249\n", + "Categories (3, object): ['UBERON:0014454', 'UBERON:0014455', 'UBERON:0019207'] tissue_ontology_term_id {}\n", + "array [2 2 2 ... 1 2 2] codes {}\n", + "string-array ['UBERON:0014454' 'UBERON:0014455' 'UBERON:0019207'] categories {}\n", + "categorical ['HsapDv:0000104', 'HsapDv:0000159', 'HsapDv:0000104', 'HsapDv:0000115', 'HsapDv:0000262', ..., 'HsapDv:0000110', 'HsapDv:0000158', 'HsapDv:0000115', 'HsapDv:0000165', 'HsapDv:0000208']\n", + "Length: 271249\n", + "Categories (40, object): ['HsapDv:0000104', 'HsapDv:0000105', 'HsapDv:0000110', 'HsapDv:0000111', ..., 'HsapDv:0000208', 'HsapDv:0000212', 'HsapDv:0000262', 'HsapDv:0000274'] development_stage_ontology_term_id {}\n", + "array [ 0 28 0 ... 5 32 36] codes {}\n", + "string-array ['HsapDv:0000104' 'HsapDv:0000105' 'HsapDv:0000110' 'HsapDv:0000111'\n", + " 'HsapDv:0000112' 'HsapDv:0000115' 'HsapDv:0000119' 'HsapDv:0000120'\n", + " 'HsapDv:0000121' 'HsapDv:0000122' 'HsapDv:0000124' 'HsapDv:0000126'\n", + " 'HsapDv:0000128' 'HsapDv:0000129' 'HsapDv:0000131' 'HsapDv:0000135'\n", + " 'HsapDv:0000137' 'HsapDv:0000140' 'HsapDv:0000141' 'HsapDv:0000144'\n", + " 'HsapDv:0000145' 'HsapDv:0000147' 'HsapDv:0000148' 'HsapDv:0000152'\n", + " 'HsapDv:0000154' 'HsapDv:0000156' 'HsapDv:0000157' 'HsapDv:0000158'\n", + " 'HsapDv:0000159' 'HsapDv:0000160' 'HsapDv:0000162' 'HsapDv:0000163'\n", + " 'HsapDv:0000165' 'HsapDv:0000166' 'HsapDv:0000171' 'HsapDv:0000207'\n", + " 'HsapDv:0000208' 'HsapDv:0000212' 'HsapDv:0000262' 'HsapDv:0000274'] categories {}\n", + "categorical ['surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', ..., 'surgical resection', 'surgical resection', NaN, 'surgical resection', 'surgical resection']\n", + "Length: 271249\n", + "Categories (1, object): ['surgical resection'] sample_collection_method {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['surgical resection'] categories {}\n", + "categorical ['Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', ..., 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', NaN, 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank']\n", + "Length: 271249\n", + "Categories (4, object): ['Baylor College of Medicine Lions Eye Bank', 'Massachusetts General Hospital', 'University of Utah', 'Utah Lions Eye Bank, Florida Lions Eye Bank'] tissue_source {}\n", + "array [ 3 3 3 ... -1 3 3] codes {}\n", + "string-array ['Baylor College of Medicine Lions Eye Bank'\n", + " 'Massachusetts General Hospital' 'University of Utah'\n", + " 'Utah Lions Eye Bank,\\xa0Florida Lions Eye Bank'] categories {}\n", + "categorical ['tissue', 'tissue', 'tissue', 'tissue', 'tissue', ..., 'tissue', 'tissue', 'tissue', 'tissue', 'tissue']\n", + "Length: 271249\n", + "Categories (1, object): ['tissue'] tissue_type {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['tissue'] categories {}\n", + "categorical ['unknown', 'unknown', 'unknown', 'unknown', 'unknown', ..., 'unknown', 'unknown', NaN, 'unknown', 'unknown']\n", + "Length: 271249\n", + "Categories (2, object): ['2020', 'unknown'] sample_collection_year {}\n", + "array [ 1 1 1 ... -1 1 1] codes {}\n", + "string-array ['2020' 'unknown'] categories {}\n", + "categorical ['mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', ..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation']\n", + "Length: 271249\n", + "Categories (3, object): ['mechanical dissociation,centrifugation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation'] suspension_derivation_process {}\n", + "array [2 2 2 ... 1 2 2] codes {}\n", + "string-array ['mechanical dissociation,centrifugation'\n", + " 'mechanical dissociation,detergent solubilization'\n", + " 'mechanical dissociation,enzymatic dissociation'] categories {}\n", + "categorical ['c9d08907-31b1-4ae7-aeb9-4d4eddfee567', 'ebb7c928-33b8-4fc2-badf-8df6bb7055e6', 'c356b586-a9e8-446e-bbc9-78b6b71dd69a', '44511e86-169f-4143-ab8f-291d826e3dbe', '6d136144-0dcf-41a2-8cc5-fff28f1e4b05', ..., '48a85fa2-e4d9-484a-a282-4b3f7b5dda17', '42e9751f-d51d-4e32-9af4-f4734e981de5', '7a99b2a1-c3f9-4b8b-bc1a-945074b49751', '1b846b54-6cac-4ff5-b9d7-7af799f01528', '1302d1b2-5bb2-4ed1-b0d7-75ff175cc4ad']\n", + "Length: 271249\n", + "Categories (104, object): 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tissue_handling_interval {}\n", + "array [18 14 18 ... -1 20 26] codes {}\n", + "string-array ['2.6 hours' '2.82 hours' '2.98 hours' '3 hours' '3.5 hours' '3.72 hours'\n", + " '3.83 hours' '3.92 hours' '4 hours' '4.8 hours' '4.15 hours' '4.55 hours'\n", + " '5 hours' '5.3 hours' '5.18 hours' '5.67 hours' '6 hours' '6.03 hours'\n", + " '6.5 hours' '6.08 hours' '6.28 hours' '6.47 hours' '7 hours' '7.43 hours'\n", + " '7.52 hours' '8 hours' '8.02 hours' '8.75 hours' '8.83 hours'\n", + " '8.92 hours' '9 hours' '9.5 hours' '9.17 hours' '10 hours' '>6 hours'\n", + " 'unknown'] categories {}\n", + "categorical ['f05bf2a3-0ff8-4029-871e-43013f55ba17', 'ddb10563-d007-40d8-9ce1-ba226de27964', '1bd8eae2-5c33-47d6-9219-004bfe8829b5', 'ce720cc1-b101-47e6-91ab-7b8d5cfb22e4', '6ec4e3b6-c85a-4fb2-98e5-ce7cae85494c', ..., 'c04612b7-bc4b-49a3-8df7-44c9a7a8d57a', '43c81dc0-8f3f-46a4-b309-55f1fc181d12', NaN, 'd5adb789-faa7-4629-9ad9-6ce56d198e42', 'bd3e9262-e276-455e-8d6c-ad86b3ebada3']\n", + "Length: 271249\n", + "Categories (82, object): ['0f127276-6374-4e99-adb9-5cf6d0cae2c7', '1bd8eae2-5c33-47d6-9219-004bfe8829b5', '1d833c17-e383-4e63-ba32-21507ac11909', '1dcac7fe-df13-4793-9de2-b3a9b6236259', ..., 'f1478d8b-b0f9-4c52-908a-2a86aeadf68d', 'fa0c4d96-399d-4cb8-a52b-974e70e0cff9', 'fb0ffcc5-7025-4629-b0b1-a8303ecddc71', 'fd806e8b-1a82-4b73-95c8-3db3ef1ec2c4'] library_id {}\n", + "array [74 67 1 ... -1 64 58] codes {}\n", + "string-array ['0f127276-6374-4e99-adb9-5cf6d0cae2c7'\n", + " '1bd8eae2-5c33-47d6-9219-004bfe8829b5'\n", + " '1d833c17-e383-4e63-ba32-21507ac11909'\n", + " '1dcac7fe-df13-4793-9de2-b3a9b6236259'\n", + " '1f09f460-3064-4441-9308-88273bfac255'\n", + " '3a378b2c-10c7-4404-ac31-449e47406228'\n", + " '3b93623e-ebf7-4ac8-a209-90739b17b571'\n", + " '3c3f290a-d718-417c-afa6-e119d999a866'\n", + " '3d84f8dc-a811-40ca-b3bb-7c18de07417c'\n", + " '4c4efeb3-09da-467f-aeff-eaf1f99b08ae'\n", + " '4cfe3922-7f3c-45d0-8cbe-6b0878084486'\n", + " 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'f05bf2a3-0ff8-4029-871e-43013f55ba17'\n", + " 'f5bf8248-ab25-4018-aa98-f4be59ee4574'\n", + " 'f7a23e1b-53a0-47b1-bc9d-48a5e9914ac6'\n", + " 'f515b49c-0528-486e-b019-0b73fba5f9a5'\n", + " 'f1478d8b-b0f9-4c52-908a-2a86aeadf68d'\n", + " 'fa0c4d96-399d-4cb8-a52b-974e70e0cff9'\n", + " 'fb0ffcc5-7025-4629-b0b1-a8303ecddc71'\n", + " 'fd806e8b-1a82-4b73-95c8-3db3ef1ec2c4'] categories {}\n", + "categorical ['EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', ..., 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922']\n", + "Length: 271249\n", + "Categories (2, object): ['EFO:0009900', 'EFO:0009922'] assay_ontology_term_id {}\n", + "array [1 1 1 ... 1 1 1] codes {}\n", + "string-array ['EFO:0009900' 'EFO:0009922'] categories {}\n", + "categorical ['3 prime tag', '3 prime tag', '3 prime tag', '3 prime tag', '3 prime tag', ..., '3 prime tag', '3 prime tag', NaN, '3 prime tag', '3 prime tag']\n", + "Length: 271249\n", + "Categories (2, object): ['3 prime tag', '5 prime tag'] sequenced_fragment {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['3 prime tag' '5 prime tag'] categories {}\n", + "categorical ['Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', ..., 'Baylor College of Medicine', 'Baylor College of Medicine', NaN, 'Baylor College of Medicine', 'Baylor College of Medicine']\n", + "Length: 271249\n", + "Categories (2, object): ['Baylor College of Medicine', 'Harvard University'] institute {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['Baylor College of Medicine' 'Harvard University'] categories {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, NaN, NaN, NaN]\n", + "Length: 271249\n", + "Categories (8, object): ['SRX20898918', 'SRX20898919', 'SRX20898920', 'SRX20898921', 'SRX20898922', 'SRX20898923', 'SRX20898924', 'SRX20898925'] library_id_repository {}\n", + "array [-1 -1 -1 ... -1 -1 -1] codes {}\n", + "string-array ['SRX20898918' 'SRX20898919' 'SRX20898920' 'SRX20898921' 'SRX20898922'\n", + " 'SRX20898923' 'SRX20898924' 'SRX20898925'] categories {}\n", + "categorical ['Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', ..., 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', NaN, 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)']\n", + "Length: 271249\n", + "Categories (1, object): ['Illumina NovaSeq 6000 (EFO:0008637)'] sequencing_platform {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['Illumina NovaSeq 6000 (EFO:0008637)'] categories {}\n", + "array [False False False ... True False False] is_primary_data {}\n", + "categorical ['CL:1000414', 'CL:1000414', 'CL:0000666', 'CL:1000414', 'CL:1000414', ..., 'CL:0000666', 'CL:0000666', 'CL:0000077', 'CL:0000666', 'CL:1000414']\n", + "Length: 271249\n", + "Categories (20, object): ['CL:0000077', 'CL:0000095', 'CL:0000097', 'CL:0000115', ..., 'CL:1000412', 'CL:1000413', 'CL:1000414', 'unknown'] cell_type_ontology_term_id {}\n", + "array [18 18 8 ... 0 8 18] codes {}\n", + "string-array ['CL:0000077' 'CL:0000095' 'CL:0000097' 'CL:0000115' 'CL:0000136'\n", + " 'CL:0000192' 'CL:0000235' 'CL:0000542' 'CL:0000666' 'CL:0000669'\n", + " 'CL:0000763' 'CL:0000988' 'CL:0002138' 'CL:0002543' 'CL:0002573'\n", + " 'CL:0009099' 'CL:1000412' 'CL:1000413' 'CL:1000414' 'unknown'] categories {}\n", + "categorical ['Venule', 'Venule', 'Fenestrated capillary', 'Venule', 'Venule', ..., 'Fenestrated capillary', 'Fenestrated capillary', 'Mesothelial Cells', 'Fenestrated capillary', 'Venule']\n", + "Length: 271249\n", + "Categories (21, object): ['Adipogenic Progenitors', 'Arterial', 'Arteriole', 'Endothelial Cells', ..., 'Smooth Muscle Cells', 'T/NK/B Cells', 'Vein', 'Venule'] author_cell_type {}\n", + "array [20 20 5 ... 11 5 20] codes {}\n", + "string-array ['Adipogenic Progenitors' 'Arterial' 'Arteriole' 'Endothelial Cells'\n", + " 'Erythroblasts - Myelocytes - Mature NK Cells' 'Fenestrated capillary'\n", + " 'Lymphatic Endothelial Cells' 'Lymphoid/B/NK Cells' 'Macrophages'\n", + " 'Mast Cells' 'Mature Adipocytes' 'Mesothelial Cells'\n", + " 'Myeloid Cells (Monocytes, Neutrophils, Macrophages)'\n", + " 'Neuronal-associated Cells' 'PRM1+ Cells' 'Pericytes' 'Schwann Cells'\n", + " 'Smooth Muscle Cells' 'T/NK/B Cells' 'Vein' 'Venule'] categories {}\n", + "categorical ['PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', ..., 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461']\n", + "Length: 271249\n", + "Categories (1, object): ['PATO:0000461'] disease_ontology_term_id {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['PATO:0000461'] categories {}\n", + "categorical ['none', 'none', 'none', 'none', 'none', ..., 'none', 'none', 'none', 'none', 'none']\n", + "Length: 271249\n", + "Categories (3, object): ['['meningeal sarcoma']', '[type 2 diabetes mellitus]', 'none'] reported_diseases {}\n", + "array [2 2 2 ... 2 2 2] codes {}\n", + "string-array [\"['meningeal sarcoma']\" '[type 2 diabetes mellitus]' 'none'] categories {}\n", + "categorical ['PATO:0000383', 'PATO:0000383', 'PATO:0000383', 'PATO:0000384', 'PATO:0000384', ..., 'PATO:0000383', 'PATO:0000384', 'PATO:0000383', 'PATO:0000383', 'PATO:0000384']\n", + "Length: 271249\n", + "Categories (2, object): ['PATO:0000383', 'PATO:0000384'] sex_ontology_term_id {}\n", + "array [0 0 0 ... 0 0 1] codes {}\n", + "string-array ['PATO:0000383' 'PATO:0000384'] categories {}\n", + "array [1662. 2402. 1746. ... nan 1724. 1266.] nCount_RNA {}\n", + "array [1090. 1329. 1112. ... nan 1127. 858.] nFeature_RNA {}\n", + "array [0.12033694 0. 0.51546392 ... nan 0.92807425 0.23696682] percent.mt {}\n", + "categorical ['Chen_lab', 'Chen_lab', 'Chen_lab', 'Chen_lab', 'Chen_lab', ..., 'Chen_lab', 'Chen_lab', NaN, 'Chen_lab', 'Chen_lab']\n", + "Length: 271249\n", + "Categories (2, object): ['Chen_lab', 'Sanes_GSE236566'] Study {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['Chen_lab' 'Sanes_GSE236566'] categories {}\n", + "categorical ['Pediatric', 'Adult', 'Pediatric', 'Adult', 'Pediatric', ..., 'Pediatric', 'Adult', NaN, 'Adult', 'Adult']\n", + "Length: 271249\n", + "Categories (2, object): ['Adult', 'Pediatric'] Developmental {}\n", + "array [ 1 0 1 ... -1 0 0] codes {}\n", + "string-array ['Adult' 'Pediatric'] categories {}\n", + "categorical ['6h30m', '5h11m', '6h30m', '6h', '10h', ..., '3h', '8h', NaN, '6h17m', '8h1m']\n", + "Length: 271249\n", + "Categories (36, object): ['2h36m', '2h49m', '2h59m', '3h', ..., '9h', '9h10m', '10h', 'Unknown'] Post_mortemtime {}\n", + "array [21 13 21 ... -1 19 27] codes {}\n", + "string-array ['2h36m' '2h49m' '2h59m' '3h' '3h30m' '3h43m' '3h50m' '3h55m' '4h' '4h9m'\n", + " '4h33m' '4h48m' '5h' '5h11m' '5h18m' '5h40m' '6h' '6h2m' '6h5m' '6h17m'\n", + " '6h28m' '6h30m' '6h+' '7h' '7h26m' '7h31m' '8h' '8h1m' '8h45m' '8h50m'\n", + " '8h55m' '9.5h' '9h' '9h10m' '10h' 'Unknown'] categories {}\n", + "categorical ['6.5', '5.18', '6.5', '6', '10', ..., '3', '8', NaN, '6.28', '8.02']\n", + "Length: 271249\n", + "Categories (36, object): ['2.6', '2.82', '2.98', '3', ..., '9.17', '10', '>6', 'Unknown'] PMT_in_hrs {}\n", + "array [18 14 18 ... -1 20 26] codes {}\n", + "string-array ['2.6' '2.82' '2.98' '3' '3.5' '3.72' '3.83' '3.92' '4' '4.8' '4.15'\n", + " '4.55' '5' '5.3' '5.18' '5.67' '6' '6.03' '6.5' '6.08' '6.28' '6.47' '7'\n", + " '7.43' '7.52' '8' '8.02' '8.75' '8.83' '8.92' '9' '9.5' '9.17' '10' '>6'\n", + " 'Unknown'] categories {}\n", + "categorical ['OD', 'OD', 'OD', 'Unknown', 'Unknown', ..., 'Unknown', 'Unknown', NaN, 'OD', 'OD']\n", + "Length: 271249\n", + "Categories (3, object): ['OD', 'OS', 'Unknown'] Eye {}\n", + "array [ 0 0 0 ... -1 0 0] codes {}\n", + "string-array ['OD' 'OS' 'Unknown'] categories {}\n", + "categorical ['Peripheral', 'Macular', 'Macular', 'Peripheral', 'Macular', ..., 'Peripheral', 'Peripheral', NaN, 'Peripheral', 'Macular']\n", + "Length: 271249\n", + "Categories (2, object): ['Macular', 'Peripheral'] Region {}\n", + "array [ 1 0 0 ... -1 1 0] codes {}\n", + "string-array ['Macular' 'Peripheral'] categories {}\n", + "categorical ['3v31_MMD_23_4292_RPE', '3v31_MMD_22-3991_Mac_RPE', '3v31_MMD_23-4291_Mac_RPE', '3v31_BCM_22_0183_RPE_WOLF', '3v31_BCM_22-0698_Mac_RPE', ..., '3v31_BCM_23_0491_RPE', '3v31_BCM_22_0500_RPE', NaN, '3v31_MMD_23_3312_RPE', '3v31_MMD_22-7151_Mac_RPE']\n", + "Length: 271249\n", + "Categories (82, object): ['3v31_22_0574_RPE', '3v31_22_0574_RPE_Tyto', '3v31_BCM_1d_fetal_RPE', '3v31_BCM_22-0396_Mac_RPE', ..., 'GSM7553466', 'GSM7553467', 'GSM7553469', 'GSM7553471'] sampleid {}\n", + "array [66 42 60 ... -1 65 43] codes {}\n", + "string-array ['3v31_22_0574_RPE' '3v31_22_0574_RPE_Tyto' '3v31_BCM_1d_fetal_RPE'\n", + " '3v31_BCM_22-0396_Mac_RPE' '3v31_BCM_22-0434_Mac_RPE'\n", + " '3v31_BCM_22-0698_Mac_RPE' '3v31_BCM_22-0769_Mac_RPE'\n", + " '3v31_BCM_22-0849_Mac_RPE' '3v31_BCM_22_0183_Mac_RPE'\n", + " '3v31_BCM_22_0183_RPE_WOLF' '3v31_BCM_22_0200_Mac_RPE'\n", + " '3v31_BCM_22_0200_RPE' '3v31_BCM_22_0389_RPE' '3v31_BCM_22_0396_RPE_WOLF'\n", + " '3v31_BCM_22_0434_RPE' '3v31_BCM_22_0434_RPE_WOLF' '3v31_BCM_22_0458_RPE'\n", + " '3v31_BCM_22_0500_RPE' '3v31_BCM_22_0769_RPE_WOLF'\n", + " '3v31_BCM_22_0784_Mac_RPE' '3v31_BCM_22_0784_RPE_WOLF'\n", + " '3v31_BCM_22_0849_RPE' '3v31_BCM_22_0890_RPE' '3v31_BCM_22_0896_RPE_WOLF'\n", + " '3v31_BCM_23-0131_Mac_RPE' '3v31_BCM_23-0231_Mac_RPE'\n", + " '3v31_BCM_23-0334_Mac_RPE' '3v31_BCM_23-1401_Mac_RPE'\n", + " '3v31_BCM_23-1430_Mac_RPE' '3v31_BCM_23-1448_Mac_RPE'\n", + " '3v31_BCM_23_0131_RPE' '3v31_BCM_23_0231_RPE' '3v31_BCM_23_0313_RPE'\n", + " '3v31_BCM_23_0334_RPE' '3v31_BCM_23_0358_RPE' '3v31_BCM_23_0491_RPE'\n", + " '3v31_MMD_19_D005_Mac_RPE' '3v31_MMD_19_D005_RPE'\n", + " '3v31_MMD_19_D008_Mac_RPE' '3v31_MMD_19_D008_RPE'\n", + " '3v31_MMD_22-3051_Mac_RPE' '3v31_MMD_22-3131_Mac_RPE'\n", + " '3v31_MMD_22-3991_Mac_RPE' '3v31_MMD_22-7151_Mac_RPE'\n", + " '3v31_MMD_22_1972_RPE' '3v31_MMD_22_2854_RPE' '3v31_MMD_22_3053_RPE'\n", + " '3v31_MMD_22_3132_RPE' '3v31_MMD_22_3872_RPE' '3v31_MMD_22_3952_RPE_1'\n", + " '3v31_MMD_22_3952_RPE_2' '3v31_MMD_22_3992_RPE' '3v31_MMD_22_4472_RPE'\n", + " '3v31_MMD_22_5352_RPE' '3v31_MMD_22_6392_RPE' '3v31_MMD_22_6432_RPE'\n", + " '3v31_MMD_22_7032_RPE' '3v31_MMD_22_7072_RPE' '3v31_MMD_22_7152_RPE'\n", + " '3v31_MMD_22_7432_RPE' '3v31_MMD_23-4291_Mac_RPE' '3v31_MMD_23_0194_RPE'\n", + " '3v31_MMD_23_334_RPE' '3v31_MMD_23_2252_RPE' '3v31_MMD_23_2292_RPE'\n", + " '3v31_MMD_23_3312_RPE' '3v31_MMD_23_4292_RPE' '3v31_MMD_23_5453_RPE'\n", + " '5v2_22_2854_per_RPE' '5v2_22_2854_per_RPE_spin' '10x3V31_22_0183_RPE_1'\n", + " '10x3V31_22_0183_RPE_2' '10x3V31_Adult_20_0948_Lobe_RPE'\n", + " '22_4472_per_RPE_Nu' 'GSM7553460' 'GSM7553461' 'GSM7553463' 'GSM7553464'\n", + " 'GSM7553466' 'GSM7553467' 'GSM7553469' 'GSM7553471'] categories {}\n", + "categorical ['endothelial cell of venule', 'endothelial cell of venule', 'fenestrated endothelial cell', 'endothelial cell of venule', 'endothelial cell of venule', ..., 'fenestrated endothelial cell', 'fenestrated endothelial cell', 'mesothelial cell', 'fenestrated endothelial cell', 'endothelial cell of venule']\n", + "Length: 271249\n", + "Categories (20, object): ['Schwann cell', 'adipocyte', 'endothelial cell', 'endothelial cell of arteriole', ..., 'pericyte', 'smooth muscle cell', 'unknown', 'vein endothelial cell'] cell_type {}\n", + "array [ 6 6 7 ... 13 7 6] codes {}\n", + "string-array ['Schwann cell' 'adipocyte' 'endothelial cell'\n", + " 'endothelial cell of arteriole' 'endothelial cell of artery'\n", + " 'endothelial cell of lymphatic vessel' 'endothelial cell of venule'\n", + " 'fenestrated endothelial cell' 'fibro/adipogenic progenitor cell'\n", + " 'hematopoietic cell' 'lymphocyte' 'macrophage' 'mast cell'\n", + " 'mesothelial cell' 'myeloid cell' 'neuron associated cell' 'pericyte'\n", + " 'smooth muscle cell' 'unknown' 'vein endothelial cell'] categories {}\n", + "categorical ['10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', ..., '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3']\n", + "Length: 271249\n", + "Categories (2, object): ['10x 5' v2', '10x 3' v3'] assay {}\n", + "array [1 1 1 ... 1 1 1] codes {}\n", + "string-array [\"10x 5' v2\" \"10x 3' v3\"] categories {}\n", + "categorical ['normal', 'normal', 'normal', 'normal', 'normal', ..., 'normal', 'normal', 'normal', 'normal', 'normal']\n", + "Length: 271249\n", + "Categories (1, object): ['normal'] disease {}\n", + "array [0 0 0 ... 0 0 0] codes {}\n", + "string-array ['normal'] categories {}\n", + "categorical ['female', 'female', 'female', 'male', 'male', ..., 'female', 'male', 'female', 'female', 'male']\n", + "Length: 271249\n", + "Categories (2, object): ['female', 'male'] sex {}\n", + "array [0 0 0 ... 0 0 1] codes {}\n", + "string-array ['female' 'male'] categories {}\n", + "categorical ['chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', ..., 'chorioretinal region', 'chorioretinal region', 'subcutaneous abdominal adipose tissue', 'chorioretinal region', 'chorioretinal region']\n", + "Length: 271249\n", + "Categories (3, object): ['chorioretinal region', 'subcutaneous abdominal adipose tissue', 'visceral abdominal adipose tissue'] tissue {}\n", + "array [0 0 0 ... 1 0 0] codes {}\n", + "string-array ['chorioretinal region' 'subcutaneous abdominal adipose tissue'\n", + " 'visceral abdominal adipose tissue'] categories {}\n", + "categorical ['African American', 'African American', 'African American', 'European', 'European', ..., 'African American', 'European', 'African American', 'African American', 'Hispanic or Latin American']\n", + "Length: 271249\n", + "Categories (6, object): ['European', 'South Asian', 'Hispanic or Latin American', 'Indian', 'African American', 'unknown'] self_reported_ethnicity {}\n", + "array [4 4 4 ... 4 4 2] codes {}\n", + "string-array ['European' 'South Asian' 'Hispanic or Latin American' 'Indian'\n", + " 'African American' 'unknown'] categories {}\n", + "categorical ['10-year-old stage', '65-year-old stage', '10-year-old stage', '21-year-old stage', 'newborn stage (0-28 days)', ..., '16-year-old stage', '64-year-old stage', '21-year-old stage', '71-year-old stage', '82-year-old stage']\n", + "Length: 271249\n", + "Categories (40, object): ['10-year-old stage', '11-year-old stage', '16-year-old stage', '17-year-old stage', ..., '82-year-old stage', '86-year-old stage', '90 year-old and over stage', 'newborn stage (0-28 days)'] development_stage {}\n", + "array [ 0 28 0 ... 5 32 36] codes {}\n", + "string-array ['10-year-old stage' '11-year-old stage' '16-year-old stage'\n", + " '17-year-old stage' '18-year-old stage' '21-year-old stage'\n", + " '25-year-old stage' '26-year-old stage' '27-year-old stage'\n", + " '28-year-old stage' '30-year-old stage' '32-year-old stage'\n", + " '34-year-old stage' '35-year-old stage' '37-year-old stage'\n", + " '41-year-old stage' '43-year-old stage' '46-year-old stage'\n", + " '47-year-old stage' '50-year-old stage' '51-year-old stage'\n", + " '53-year-old stage' '54-year-old stage' '58-year-old stage'\n", + " '60-year-old stage' '62-year-old stage' '63-year-old stage'\n", + " '64-year-old stage' '65-year-old stage' '66-year-old stage'\n", + " '68-year-old stage' '69-year-old stage' '71-year-old stage'\n", + " '72-year-old stage' '77-year-old stage' '81-year-old stage'\n", + " '82-year-old stage' '86-year-old stage' '90 year-old and over stage'\n", + " 'newborn stage (0-28 days)'] categories {}\n", + "string-array ['WvwV68V!*6' 'VDY0p`o_;k' 'RT8u$f3J6y' ... 'ug{*mFhqtP' '((KWHh!1^H'\n", + " 'kesisG#am%'] observation_joinid {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'GENCODE 32', NaN, NaN]\n", + "Length: 271249\n", + "Categories (1, object): ['GENCODE 32'] mapped_reference_annotation {}\n", + "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", + "string-array ['GENCODE 32'] categories {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'c3516e93-6857-4fb2-8eab-31038dbab88d', NaN, NaN]\n", + "Length: 271249\n", + "Categories (22, object): ['0a5ca5af-a3ba-4f57-a692-c1c585051aec', '1fc35617-2b40-498b-9060-4f0a911ae941', '3adc1917-d13f-47ed-a76d-361cd6d2c790', '07c898fe-dc65-4550-b68e-967fc10861cf', ..., 'e1abc275-33f0-4198-8b08-c71f82d1fbd6', 'e4fd6c96-fbde-46a4-a749-368dbd372dab', 'ee2af55d-a295-4b3f-8f2e-3b95d3d62a22', 'f3668d06-5641-4ba5-bcbe-d18a7bb9b4e7'] sample_uuid {}\n", + "array [-1 -1 -1 ... 13 -1 -1] codes {}\n", + "string-array ['0a5ca5af-a3ba-4f57-a692-c1c585051aec'\n", + " 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{}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, '20 minute', NaN, NaN]\n", + "Length: 271249\n", + "Categories (1, object): ['20 minute'] suspension_dissociation_time {}\n", + "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", + "string-array ['20 minute'] categories {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, '158fa263-4d48-4894-96e2-69eba15c4c5f', NaN, NaN]\n", + "Length: 271249\n", + "Categories (22, object): ['0eb623da-699f-4cf9-8c1f-d610b6898c53', '1e290323-810e-4202-9da8-097a90553768', '3df6c15b-fc26-437f-820f-0ec3a771990f', '4b9e7151-7395-4b1f-8c9b-2033f6658a54', ..., '90113f89-09cc-49e6-9792-1df25602e7ad', '20027346-e846-46db-91c7-0574419aedda', 'a3855ec2-6539-42e0-b663-3af74aec8b81', 'bb10ba9e-5405-46f7-bf85-f1eb11467574'] library_uuid {}\n", + "array [-1 -1 -1 ... 15 -1 -1] codes {}\n", + "string-array ['0eb623da-699f-4cf9-8c1f-d610b6898c53'\n", + " '1e290323-810e-4202-9da8-097a90553768'\n", + " '3df6c15b-fc26-437f-820f-0ec3a771990f'\n", + " 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271249\n", + "Categories (1, object): ['10000 nuclei'] library_starting_quantity {}\n", + "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", + "string-array ['10000 nuclei'] categories {}\n", + "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, '7', NaN, NaN]\n", + "Length: 271249\n", + "Categories (19, object): ['0', '1', '2', '3', ..., '15', '16', '17', '18'] leiden_scVI {}\n", + "array [-1 -1 -1 ... 7 -1 -1] codes {}\n", + "string-array ['0' '1' '2' '3' '4' '5' '6' '7' '8' '9' '10' '11' '12' '13' '14' '15'\n", + " '16' '17' '18'] categories {}\n", + "dataframe Empty DataFrame\n", + "Columns: []\n", + "Index: [ENSG00000000003, ENSG00000000005, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000000938, ENSG00000000971, ENSG00000001036, ENSG00000001084, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001561, ENSG00000001617, ENSG00000001626, ENSG00000001629, ENSG00000001630, ENSG00000001631, ENSG00000002016, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002726, ENSG00000002745, ENSG00000002746, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000002933, ENSG00000003056, ENSG00000003096, ENSG00000003137, ENSG00000003147, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003756, ENSG00000003987, ENSG00000003989, ENSG00000004059, ENSG00000004139, ENSG00000004142, ENSG00000004399, ENSG00000004455, ENSG00000004468, ENSG00000004478, ENSG00000004487, ENSG00000004534, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004776, ENSG00000004777, ENSG00000004779, ENSG00000004799, ENSG00000004809, ENSG00000004838, ENSG00000004846, ENSG00000004848, ENSG00000004864, ENSG00000004866, ENSG00000004897, ENSG00000004939, ENSG00000004948, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG00000005100, ENSG00000005102, ENSG00000005108, ENSG00000005156, ENSG00000005175, ENSG00000005187, ENSG00000005189, ENSG00000005194, ENSG00000005206, ENSG00000005238, ENSG00000005243, ENSG00000005249, ENSG00000005302, ENSG00000005339, ENSG00000005379, ENSG00000005381, ENSG00000005421, ENSG00000005436, ENSG00000005448, ENSG00000005469, ENSG00000005471, ENSG00000005483, ...]\n", + "\n", + "[36406 rows x 0 columns] var {}\n", + "string-array ['ENSG00000000003' 'ENSG00000000005' 'ENSG00000000419' ...\n", + " 'ENSG00000289604' 'ENSG00000290292' 'ENSG00000291237'] _index {}\n", + "dict {'X_scVI': array([[-1.77993611e-01, 8.61403346e-03, -7.60306045e-03, ...,\n", + " -1.92724898e-01, -6.83587313e-01, -7.36990944e-04],\n", + " [-5.73522449e-01, -9.81938560e-03, -1.75076518e-02, ...,\n", + " 4.91404831e-02, 3.27884197e-01, 2.22777352e-02],\n", + " [ 4.30468947e-01, 2.83498019e-02, 1.39225218e-02, ...,\n", + " 3.56718922e+00, 1.27075166e-02, -2.55109631e-02],\n", + " ...,\n", + " [-3.99452448e-02, -2.92961951e-03, -3.55084419e-01, ...,\n", + " nan, nan, nan],\n", + " [-1.37655306e+00, 1.46282688e-02, -2.16566212e-03, ...,\n", + " 6.89336777e-01, -3.31150651e-01, 1.24030635e-02],\n", + " [-1.87925138e-02, 1.25729386e-03, -4.77777235e-03, ...,\n", + " 1.54537106e+00, -3.73984814e-01, -1.24053285e-02]],\n", + " shape=(271249, 100), dtype=float32), 'X_umap': array([[ 9.051687 , 5.5358324 ],\n", + " [ 9.444352 , 3.9529152 ],\n", + " [ 3.8349276 , -0.57459825],\n", + " ...,\n", + " [-3.9295218 , 9.292584 ],\n", + " [ 6.20132 , 1.9481294 ],\n", + " [ 9.776284 , 5.017546 ]], shape=(271249, 2), dtype=float32)} obsm {}\n", + "array [[-1.77993611e-01 8.61403346e-03 -7.60306045e-03 ... -1.92724898e-01\n", + " -6.83587313e-01 -7.36990944e-04]\n", + " [-5.73522449e-01 -9.81938560e-03 -1.75076518e-02 ... 4.91404831e-02\n", + " 3.27884197e-01 2.22777352e-02]\n", + " [ 4.30468947e-01 2.83498019e-02 1.39225218e-02 ... 3.56718922e+00\n", + " 1.27075166e-02 -2.55109631e-02]\n", + " ...\n", + " [-3.99452448e-02 -2.92961951e-03 -3.55084419e-01 ... nan\n", + " nan nan]\n", + " [-1.37655306e+00 1.46282688e-02 -2.16566212e-03 ... 6.89336777e-01\n", + " -3.31150651e-01 1.24030635e-02]\n", + " [-1.87925138e-02 1.25729386e-03 -4.77777235e-03 ... 1.54537106e+00\n", + " -3.73984814e-01 -1.24053285e-02]] X_scVI {'shards': (270336, 100), 'chunks': (1024, 100), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "array [[ 9.051687 5.5358324 ]\n", + " [ 9.444352 3.9529152 ]\n", + " [ 3.8349276 -0.57459825]\n", + " ...\n", + " [-3.9295218 9.292584 ]\n", + " [ 6.20132 1.9481294 ]\n", + " [ 9.776284 5.017546 ]] X_umap {'shards': (270336, 2), 'chunks': (1024, 2), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", + "dict {} varm {}\n", + "dict {} obsp {}\n", + "dict {} varp {}\n", + "dict {} layers {}\n", + "dict {} uns {}\n", + "raw Raw AnnData with n_obs × n_vars = 271249 × 36406 raw {}\n", + "csr_matrix \n", + " Coords\tValues\n", + " (0, 6381)\t0.0\n", + " (0, 7766)\t0.0\n", + " (0, 8748)\t0.0\n", + " (0, 8975)\t0.0\n", + " (0, 12475)\t0.0\n", + " (0, 12479)\t0.0\n", + " (0, 12481)\t0.0\n", + " (0, 13841)\t0.0\n", + " (0, 14274)\t0.0\n", + " (0, 14909)\t0.0\n", + " (0, 16128)\t0.0\n", + " (0, 17261)\t0.0\n", + " (0, 17271)\t0.0\n", + " (0, 17497)\t0.0\n", + " (0, 17896)\t0.0\n", + " (0, 18254)\t0.0\n", + " (0, 18515)\t0.0\n", + " (0, 18518)\t0.0\n", + " (0, 18532)\t0.0\n", + " (0, 18743)\t0.0\n", + " (0, 18745)\t0.0\n", + " (0, 18769)\t0.0\n", + " (0, 18790)\t0.0\n", + " (0, 18794)\t0.0\n", + " (0, 18807)\t0.0\n", + " :\t:\n", + " (271248, 14024)\t5.0\n", + " (271248, 4718)\t2.0\n", + " (271248, 15390)\t2.0\n", + " (271248, 4666)\t1.0\n", + " (271248, 1878)\t1.0\n", + " (271248, 5874)\t3.0\n", + " (271248, 714)\t1.0\n", + " (271248, 8744)\t1.0\n", + " (271248, 4540)\t2.0\n", + " (271248, 10607)\t1.0\n", + " (271248, 4525)\t1.0\n", + " (271248, 15093)\t1.0\n", + " (271248, 12417)\t1.0\n", + " (271248, 6650)\t1.0\n", + " (271248, 16129)\t1.0\n", + " (271248, 16297)\t1.0\n", + " (271248, 8169)\t2.0\n", + " (271248, 5696)\t1.0\n", + " (271248, 8185)\t1.0\n", + " (271248, 10613)\t1.0\n", + " (271248, 10141)\t1.0\n", + " (271248, 642)\t1.0\n", + " (271248, 17141)\t1.0\n", + " (271248, 8153)\t4.0\n", + " (271248, 4520)\t2.0 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ubuntu/home_drive/volume/arrayloaders/venv/lib/python3.12/site-packages/zarr/api/asynchronous.py:244: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.\n", + " warnings.warn(\n", + "100%|██████████| 1/1 [00:40<00:00, 40.62s/it]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dataframe Empty DataFrame\n", + "Columns: []\n", + "Index: [ENSG00000000003, ENSG00000000005, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000000938, ENSG00000000971, ENSG00000001036, ENSG00000001084, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001561, ENSG00000001617, ENSG00000001626, ENSG00000001629, ENSG00000001630, ENSG00000001631, ENSG00000002016, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002726, ENSG00000002745, ENSG00000002746, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000002933, ENSG00000003056, ENSG00000003096, ENSG00000003137, ENSG00000003147, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003756, ENSG00000003987, ENSG00000003989, ENSG00000004059, ENSG00000004139, ENSG00000004142, ENSG00000004399, ENSG00000004455, ENSG00000004468, ENSG00000004478, ENSG00000004487, ENSG00000004534, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004776, ENSG00000004777, ENSG00000004779, ENSG00000004799, ENSG00000004809, ENSG00000004838, ENSG00000004846, ENSG00000004848, ENSG00000004864, ENSG00000004866, ENSG00000004897, ENSG00000004939, ENSG00000004948, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG00000005100, ENSG00000005102, ENSG00000005108, ENSG00000005156, ENSG00000005175, ENSG00000005187, ENSG00000005189, ENSG00000005194, ENSG00000005206, ENSG00000005238, ENSG00000005243, ENSG00000005249, ENSG00000005302, ENSG00000005339, ENSG00000005379, ENSG00000005381, ENSG00000005421, ENSG00000005436, ENSG00000005448, ENSG00000005469, ENSG00000005471, ENSG00000005483, ...]\n", + "\n", + "[36406 rows x 0 columns] var {}\n", + "string-array ['ENSG00000000003' 'ENSG00000000005' 'ENSG00000000419' ...\n", + " 'ENSG00000289604' 'ENSG00000290292' 'ENSG00000291237'] _index {}\n", + "dict {} varm {}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + } + ], "source": [ "from annbatch import add_to_collection\n", "\n", @@ -227,7 +2582,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3.9.12 ('squidpy39')", + "display_name": "venv", "language": "python", "name": "python3" }, @@ -241,12 +2596,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" - }, - "vscode": { - "interpreter": { - "hash": "ae6466e8d4f517858789b5c9e8f0ed238fb8964458a36305fca7bddc149e9c64" - } + "version": "3.12.6" } }, "nbformat": 4, From 59e2642d9915dfbe390e5bc4dd79d71f22ad96cd Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Thu, 9 Oct 2025 10:54:02 +0000 Subject: [PATCH 15/15] chore: clean rerun --- docs/notebooks/example.ipynb | 2271 +--------------------------------- 1 file changed, 12 insertions(+), 2259 deletions(-) diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index 726da4b..6ffa0ce 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -80,7 +80,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 1, @@ -143,1117 +143,15 @@ "name": "stderr", "output_type": "stream", "text": [ - "/mnt/volume/arrayloaders/src/annbatch/io.py:214: UserWarning: Some anndatas have raw and others do not, consider deleting raw via transform_input_adata\n", + "/mnt/volume/arrayloaders/src/annbatch/io.py:228: UserWarning: Some anndatas have layers keys not present in others' layers, consider stopping and using the `transform_input_adata` argument to alter layers accordingly.\n", " adata_concat = _lazy_load_with_obs_var_in_memory(adata_paths)\n", " 0%| | 0/1 [00:00 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "csr_matrix \n", - " Coords\tValues\n", - " (0, 6381)\t0.0\n", - " (0, 7766)\t0.0\n", - " (0, 8748)\t0.0\n", - " (0, 8975)\t0.0\n", - " (0, 12475)\t0.0\n", - " (0, 12479)\t0.0\n", - " (0, 12481)\t0.0\n", - " (0, 13841)\t0.0\n", - " (0, 14274)\t0.0\n", - " (0, 14909)\t0.0\n", - " (0, 16128)\t0.0\n", - " (0, 17261)\t0.0\n", - " (0, 17271)\t0.0\n", - " (0, 17497)\t0.0\n", - " (0, 17896)\t0.0\n", - " (0, 18254)\t0.0\n", - " (0, 18515)\t0.0\n", - " (0, 18518)\t0.0\n", - " (0, 18532)\t0.0\n", - " (0, 18743)\t0.0\n", - " (0, 18745)\t0.0\n", - " (0, 18769)\t0.0\n", - " (0, 18790)\t0.0\n", - " (0, 18794)\t0.0\n", - " (0, 18807)\t0.0\n", - " :\t:\n", - " (986, 36077)\t0.0\n", - " (986, 36088)\t0.0\n", - " (986, 36101)\t0.0\n", - " (986, 36114)\t0.0\n", - " (986, 36120)\t0.0\n", - " (986, 36133)\t0.0\n", - " (986, 36140)\t0.0\n", - " (986, 36143)\t0.0\n", - " (986, 36149)\t0.0\n", - " (986, 36158)\t0.0\n", - " (986, 36179)\t0.0\n", - " (986, 36211)\t0.0\n", - " (986, 36214)\t0.0\n", - " (986, 36224)\t0.0\n", - " (986, 36244)\t0.0\n", - " (986, 36269)\t0.0\n", - " (986, 36285)\t0.0\n", - " (986, 36310)\t0.0\n", - " (986, 36318)\t0.0\n", - " (986, 36363)\t0.0\n", - " (986, 36373)\t0.0\n", - " (986, 35974)\t1.443677544593811\n", - " (986, 36296)\t1.443677544593811\n", - " (986, 36393)\t2.011228561401367\n", - " (986, 36075)\t1.443677544593811 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "dataframe reference_genome \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 GRCh38 \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 GRCh38 \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 GRCh38 \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 GRCh38 \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 GRCh38 \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 GRCh38 \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 GRCh38 \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 GRCh38 \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " gene_annotation_version \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 v98 \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 v98 \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 v98 \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 v98 \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 v98 \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 v98 \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 v98 \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 v98 \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " alignment_software \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 Cell Ranger count v7.1.0 \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 Cell Ranger count v7.1.0 \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 Cell Ranger count v7.1.0 \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 Cell Ranger count v7.1.0 \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " intronic_reads_counted \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 yes \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 yes \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 yes \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 yes \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 yes \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 yes \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 yes \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 yes \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " donor_id donor_age \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 BCM_22_0698 1 day \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 MMD_22_16860 60 years \n", - "CCACACTGTGGGCTTC-1-01_OM donor-TREE NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 BCM_23_1430 >89 years \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 BCM_22_0890 64 years \n", - "... ... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 MMD_23_17738 10 years \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 BCM_22_0698 1 day \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 BCM_23_0313 60 years \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 BCM_22_0458 25 years \n", - "CAACCTCAGTTGAATG-1-05_OM donor-PINK NaN \n", - "\n", - " self_reported_ethnicity_ontology_term_id \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 HANCESTRO:0005 \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 HANCESTRO:0568 \n", - "CCACACTGTGGGCTTC-1-01_OM HANCESTRO:0005 \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 HANCESTRO:0568 \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 HANCESTRO:0487 \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 HANCESTRO:0568 \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 HANCESTRO:0005 \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 HANCESTRO:0005 \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 HANCESTRO:0014 \n", - "CAACCTCAGTTGAATG-1-05_OM HANCESTRO:0568 \n", - "\n", - " donor_cause_of_death \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 unknown \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 unknown \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 unknown \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 unknown \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 unknown \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 unknown \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 unknown \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 unknown \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " donor_living_at_sample_collection \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 False \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 False \n", - "CCACACTGTGGGCTTC-1-01_OM True \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 False \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 False \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 False \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 False \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 False \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 False \n", - "CAACCTCAGTTGAATG-1-05_OM True \n", - "\n", - " sample_id \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 356c1cec-5dfc-4ed4-b07d-2f4b09dbc260 \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 01f33d4c-77df-4e82-b8c0-62d8c11a6e49 \n", - "CCACACTGTGGGCTTC-1-01_OM NaN \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 3306e8fd-b8c5-4d15-aac1-b31daa9e86b7 \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 02be6452-fe86-4589-84a2-cbb26954a76f \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 27848b53-eddb-44d6-894f-070488287fc2 \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 e322b3ae-fdee-462a-a4b3-37009212d7ed \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 f768fecc-f180-420c-9b86-672ad0233e18 \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 654adbbe-18f1-42ea-944b-8aa5f5848567 \n", - "CAACCTCAGTTGAATG-1-05_OM NaN \n", - "\n", - " ... mapped_reference_annotation \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 ... NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 ... NaN \n", - "CCACACTGTGGGCTTC-1-01_OM ... GENCODE 32 \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 ... NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 ... NaN \n", - "... ... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 ... NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 ... NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 ... NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 ... NaN \n", - "CAACCTCAGTTGAATG-1-05_OM ... GENCODE 32 \n", - "\n", - " sample_uuid \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM e1abc275-33f0-4198-8b08-c71f82d1fbd6 \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 1fc35617-2b40-498b-9060-4f0a911ae941 \n", - "\n", - " sample_derivation_process \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM dissection \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM dissection \n", - "\n", - " sample_source \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM Brigham and Women's Hospital \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM Brigham and Women's Hospital \n", - "\n", - " donor_BMI_at_collection \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM 59.7 \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 46.9 \n", - "\n", - " suspension_dissociation_reagent \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM Cytoplasmic cell lysis buffer \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM Cytoplasmic cell lysis buffer \n", - "\n", - " suspension_dissociation_time \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM 20 minute \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 20 minute \n", - "\n", - " library_uuid \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM 20027346-e846-46db-91c7-0574419aedda \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 4c67c43b-e36c-4efc-8469-cd9619280c98 \n", - "\n", - " library_starting_quantity \\\n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM 10000 nuclei \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 10000 nuclei \n", - "\n", - " leiden_scVI \n", - "3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1 NaN \n", - "3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1 NaN \n", - "CCACACTGTGGGCTTC-1-01_OM 4 \n", - "3v31_BCM_23-1430_Mac_RPE_GAGTGTTAGAGGTTTA-1 NaN \n", - "3v31_BCM_22_0890_RPE_CATGCGGCAGACGGAT-1 NaN \n", - "... ... \n", - "3v31_MMD_23-4291_Mac_RPE_CAGAGCCCATTACTCT-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_CTGTACCGTCAAGCGA-1 NaN \n", - "3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1 NaN \n", - "3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1 NaN \n", - "CAACCTCAGTTGAATG-1-05_OM 7 \n", - "\n", - "[171792 rows x 61 columns] obs {}\n", - "string-array ['3v31_BCM_1d_fetal_RPE_AGGGCTCCAGACTCTA-1'\n", - " '3v31_MMD_23_2292_RPE_CCTCCTCAGCGTGTCC-1' 'CCACACTGTGGGCTTC-1-01_OM' ...\n", - " '3v31_BCM_23_0313_RPE_GGGTCACCAACCGCTG-1'\n", - " '3v31_BCM_22_0458_RPE_CAATACGAGTGCGCTC-1' 'CAACCTCAGTTGAATG-1-05_OM'] _index {}\n", - "categorical ['GRCh38', 'GRCh38', NaN, 'GRCh38', 'GRCh38', ..., 'GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', NaN]\n", - "Length: 171792\n", - "Categories (1, object): ['GRCh38'] reference_genome {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['GRCh38'] categories {}\n", - "categorical ['v98', 'v98', NaN, 'v98', 'v98', ..., 'v98', 'v98', 'v98', 'v98', NaN]\n", - "Length: 171792\n", - "Categories (1, object): ['v98'] gene_annotation_version {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['v98'] categories {}\n", - "categorical ['Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN, 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', ..., 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['Cell Ranger count v7.0.1', 'Cell Ranger count v7.1.0'] alignment_software {}\n", - "array [ 1 1 -1 ... 1 1 -1] codes {}\n", - "string-array ['Cell Ranger count v7.0.1' 'Cell Ranger count v7.1.0'] categories {}\n", - "categorical ['yes', 'yes', NaN, 'yes', 'yes', ..., 'yes', 'yes', 'yes', 'yes', NaN]\n", - "Length: 171792\n", - "Categories (1, object): ['yes'] intronic_reads_counted {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['yes'] categories {}\n", - "categorical ['BCM_22_0698', 'MMD_22_16860', 'donor-TREE', 'BCM_23_1430', 'BCM_22_0890', ..., 'MMD_23_17738', 'BCM_22_0698', 'BCM_23_0313', 'BCM_22_0458', 'donor-PINK']\n", - "Length: 171792\n", - "Categories (71, object): ['BCM_21_0948', 'BCM_22_0183', 'BCM_22_0200', 'BCM_22_0396', ..., 'donor-SILK', 'donor-TIME', 'donor-TREE', 'donor-ZONE'] donor_id {}\n", - "array [ 7 33 69 ... 15 5 66] codes {}\n", - "string-array ['BCM_21_0948' 'BCM_22_0183' 'BCM_22_0200' 'BCM_22_0396' 'BCM_22_0434'\n", - " 'BCM_22_0458' 'BCM_22_0500' 'BCM_22_0698' 'BCM_22_0769' 'BCM_22_0784'\n", - " 'BCM_22_0849' 'BCM_22_0890' 'BCM_22_0896' 'BCM_23_0131' 'BCM_23_0231'\n", - " 'BCM_23_0313' 'BCM_23_0334' 'BCM_23_0358' 'BCM_23_0491' 'BCM_23_0574'\n", - " 'BCM_23_1401' 'BCM_23_1430' 'BCM_23_1448' 'Hu13' 'Hu0218' 'Hu0220'\n", - " 'Hu0222' 'Hu0235' 'MMD_19_D005' 'MMD_19_D008' 'MMD_22_13066'\n", - " 'MMD_22_14307' 'MMD_22_16608' 'MMD_22_16860' 'MMD_22_17017'\n", - " 'MMD_22_17464' 'MMD_22_17939' 'MMD_22_20137' 'MMD_22_20357'\n", - " 'MMD_22_20372' 'MMD_22_21878' 'MMD_22_25357' 'MMD_22_33472'\n", - " 'MMD_22_34032' 'MMD_22_37089' 'MMD_22_37117' 'MMD_22_38029'\n", - " 'MMD_22_38453' 'MMD_23_01524' 'MMD_23_02177' 'MMD_23_17738'\n", - " 'MMD_23_21999' 'donor-APEX' 'donor-BLUE' 'donor-BOAT' 'donor-CORK'\n", - " 'donor-COST' 'donor-DOVE' 'donor-DOWN' 'donor-GOLD' 'donor-KEYS'\n", - " 'donor-KISS' 'donor-LACE' 'donor-OATS' 'donor-PASS' 'donor-PIKE'\n", - " 'donor-PINK' 'donor-SILK' 'donor-TIME' 'donor-TREE' 'donor-ZONE'] categories {}\n", - "categorical ['1 day', '60 years', NaN, '>89 years', '64 years', ..., '10 years', '1 day', '60 years', '25 years', NaN]\n", - "Length: 171792\n", - "Categories (31, object): ['1 day', '10 years', '11 years', '16 years', ..., '81 years', '82 years', '86 years', '>89 years'] donor_age {}\n", - "array [ 0 17 -1 ... 17 6 -1] codes {}\n", - "string-array ['1 day' '10 years' '11 years' '16 years' '17 years' '21 years' '25 years'\n", - " '27 years' '30 years' '32 years' '34 years' '43 years' '46 years'\n", - " '47 years' '50 years' '53 years' '58 years' '60 years' '62 years'\n", - " '63 years' '64 years' '65 years' '68 years' '69 years' '71 years'\n", - " '72 years' '77 years' '81 years' '82 years' '86 years' '>89 years'] categories {}\n", - "categorical ['HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0487', ..., 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0005', 'HANCESTRO:0014', 'HANCESTRO:0568']\n", - "Length: 171792\n", - "Categories (6, object): ['HANCESTRO:0005', 'HANCESTRO:0006', 'HANCESTRO:0014', 'HANCESTRO:0487', 'HANCESTRO:0568', 'unknown'] self_reported_ethnicity_ontology_term_id {}\n", - "array [0 4 0 ... 0 2 4] codes {}\n", - "string-array ['HANCESTRO:0005' 'HANCESTRO:0006' 'HANCESTRO:0014' 'HANCESTRO:0487'\n", - " 'HANCESTRO:0568' 'unknown'] categories {}\n", - "categorical ['unknown', 'unknown', NaN, 'unknown', 'unknown', ..., 'unknown', 'unknown', 'unknown', 'unknown', NaN]\n", - "Length: 171792\n", - "Categories (5, object): ['Coronary Artery Disease', 'Malignant Neoplasm', 'Meningeal Sarcoma', 'Septicemia', 'unknown'] donor_cause_of_death {}\n", - "array [ 4 4 -1 ... 4 4 -1] codes {}\n", - "string-array ['Coronary Artery Disease' 'Malignant Neoplasm' 'Meningeal Sarcoma'\n", - " 'Septicemia' 'unknown'] categories {}\n", - "categorical ['False', 'False', 'True', 'False', 'False', ..., 'False', 'False', 'False', 'False', 'True']\n", - "Length: 171792\n", - "Categories (2, object): ['False', 'True'] donor_living_at_sample_collection {}\n", - "array [0 0 1 ... 0 0 1] codes {}\n", - "string-array ['False' 'True'] categories {}\n", - "categorical ['356c1cec-5dfc-4ed4-b07d-2f4b09dbc260', '01f33d4c-77df-4e82-b8c0-62d8c11a6e49', NaN, '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7', '02be6452-fe86-4589-84a2-cbb26954a76f', ..., '27848b53-eddb-44d6-894f-070488287fc2', 'e322b3ae-fdee-462a-a4b3-37009212d7ed', 'f768fecc-f180-420c-9b86-672ad0233e18', '654adbbe-18f1-42ea-944b-8aa5f5848567', NaN]\n", - "Length: 171792\n", - "Categories (74, object): ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49', '01ffac9d-c058-47a0-969a-cb8fb51ffd03', '02be6452-fe86-4589-84a2-cbb26954a76f', '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce', ..., 'ed6fd53b-c1c3-49db-b1bb-112362a63b08', 'f86e512c-166d-41fc-b41c-b7baf70709a5', 'f768fecc-f180-420c-9b86-672ad0233e18', 'f932e7b5-1e6e-435d-8ad0-f340287da943'] sample_id {}\n", - "array [26 0 -1 ... 72 28 -1] codes {}\n", - "string-array ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49'\n", - " '01ffac9d-c058-47a0-969a-cb8fb51ffd03'\n", - " '02be6452-fe86-4589-84a2-cbb26954a76f'\n", - " '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce'\n", - " '5a2a6a3c-8f15-4eab-b2d1-7a6082659a83'\n", - " '5ae43655-e166-4c87-a0fd-13ee2eb525fc'\n", - " '5b839bc9-40f6-4b83-a039-2c424c917971'\n", - " '6a0b4dbd-5147-40ea-998a-3d578ae97d11'\n", - " '6fa3060a-d2b5-4cef-893f-f0b1f523ecc1'\n", - " '8e799a46-d8e2-4e72-a483-414168d778b5'\n", - " '9bc800be-b52f-485e-935b-b5bdda9fc5b8'\n", - " '12b49488-2f2d-4626-bffa-94aee3877981'\n", - " '24d12edd-fd54-4f44-9d21-63ee3c6fc807'\n", - " '25cc7497-b4b6-40e4-88ef-c0a2fe56a3ad'\n", - " '26bf8386-4a13-4fbc-8ff3-e85230a443a3'\n", - " '51e6ba30-757c-4c86-8492-16844de41645'\n", - " '54eb2056-e459-4edb-8bc8-d6adba201d61'\n", - " '55c1fb02-40ca-462c-8578-9196e3c83f89'\n", - " '64fff8e1-8db7-42e4-85df-b76ab1727414'\n", - " '67d22e15-0d05-4c65-bda4-9cb350949266'\n", - " '70df48a7-3d69-46e7-bacd-cdebc9bb6298'\n", - " '87ce0e14-0df9-4d53-99ba-9f1ebca7de9f'\n", - " '90b737c6-9ac7-4f8c-9efc-465a67874a63'\n", - " '136c4a3b-4502-4e7b-8851-fe332faf844c'\n", - " '242cabad-f81d-4fd7-8df7-fe0b318b6c34'\n", - " '245f8d19-2496-4fc0-953c-e202e74397a7'\n", - " '356c1cec-5dfc-4ed4-b07d-2f4b09dbc260'\n", - " '616d8f67-6128-4f7a-b2b3-8205f3d7d72d'\n", - " '654adbbe-18f1-42ea-944b-8aa5f5848567'\n", - " '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7'\n", - " '4722f3bd-2909-4026-b0b9-c471f4455658'\n", - " '9383cb3d-f39c-48c7-b0d6-6cfc26307523'\n", - " '16565f49-122b-4ae2-93b2-c772d76fa697'\n", - " '27848b53-eddb-44d6-894f-070488287fc2'\n", - " '46737bca-3ca2-451d-96fb-ebb433159f41'\n", - " '47201e9a-732d-4bfa-9279-2dea84738e2b'\n", - " '71357c06-8ba6-4b26-bd1a-531c84a9c589'\n", - " '91523cbf-a9f1-4451-8dec-53528db17ca0'\n", - " '632242f1-c6e3-4e8e-926e-c4973fd4e695'\n", - " '717599fd-3926-428e-be6a-a959904b7c1a'\n", - " '994416c8-9bc5-4c1c-9d7c-379d4b53b573'\n", - " '4826577c-c1a3-4c38-bb75-fdce5e6bec62'\n", - " '5586185c-a422-4441-a069-8bc8c652a347'\n", - " '76993467-f2ba-47ff-a967-fa5fbd373f81'\n", - " 'a2b49712-d112-443c-b144-51bf0c54875e'\n", - " 'a9df5458-8c11-4e0b-a3a5-aea273628f77'\n", - " 'a77bec3b-125a-4e1e-9559-739a1adb2e6b'\n", - " 'a89c72dd-c1bf-4029-95d1-b536fb1d71fc'\n", - " 'a3221835-bb93-41c7-a346-2e865b7ab0f4'\n", - " 'ac44c485-ca45-4d66-97fe-6e57b5f2d596'\n", - " 'ae8cde23-b13a-4d9c-80c3-7ea83ee3c9c1'\n", - " 'b0f3f8b7-7f1e-4f5b-95e1-bffc6768706e'\n", - " 'b1dfa534-8408-4be9-99ff-7786f212ea85'\n", - " 'b9ff532d-9b1e-4db9-a69b-546881161bc9'\n", - " 'b30f2bdb-b49e-4464-aa85-046405e04b64'\n", - " 'c5d8d707-3bac-48ce-b65c-224eb5fd452d'\n", - " 'c41fee38-b774-414d-808d-2264e9e008f8'\n", - " 'c46e21e1-edd7-4375-a3a7-c572b3049643'\n", - " 'c934ed75-6076-461d-90ad-03cb05722656'\n", - " 'c48684a8-64af-4cfd-b27f-bcdb57a7b50e'\n", - " 'cb51c83e-0e40-40c7-992a-d08aa2f723b7'\n", - " 'cea8e120-51db-44d0-833a-3745263db2ed'\n", - " 'cf31224c-d03a-4d8a-bdef-6ea449f2d5bf'\n", - " 'd764bae0-929a-4c88-ab6b-671050059c32'\n", - " 'd5182d45-c110-4fae-bed0-58d1a6208820'\n", - " 'dbe62368-43f4-41ed-a2e7-7d696b5f19d2'\n", - " 'dcdbb48e-575b-436d-a3bf-271d2625bb64'\n", - " 'dd9809d7-f120-46e6-af75-d6cdb93115ea'\n", - " 'e322b3ae-fdee-462a-a4b3-37009212d7ed'\n", - " 'e696ec77-06d7-4e17-83fa-2d97499b7e68'\n", - " 'ed6fd53b-c1c3-49db-b1bb-112362a63b08'\n", - " 'f86e512c-166d-41fc-b41c-b7baf70709a5'\n", - " 'f768fecc-f180-420c-9b86-672ad0233e18'\n", - " 'f932e7b5-1e6e-435d-8ad0-f340287da943'] categories {}\n", - "categorical ['frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', ..., 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing']\n", - "Length: 171792\n", - "Categories (2, object): ['flash-freezing', 'frozen in liquid nitrogen'] sample_preservation_method {}\n", - "array [1 1 0 ... 1 1 0] codes {}\n", - "string-array ['flash-freezing' 'frozen in liquid nitrogen'] categories {}\n", - "categorical ['UBERON:0019207', 'UBERON:0019207', 'UBERON:0014454', 'UBERON:0019207', 'UBERON:0019207', ..., 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0014454']\n", - "Length: 171792\n", - "Categories (3, object): ['UBERON:0014454', 'UBERON:0014455', 'UBERON:0019207'] tissue_ontology_term_id {}\n", - "array [2 2 0 ... 2 2 0] codes {}\n", - "string-array ['UBERON:0014454' 'UBERON:0014455' 'UBERON:0019207'] categories {}\n", - "categorical ['HsapDv:0000262', 'HsapDv:0000154', 'HsapDv:0000160', 'HsapDv:0000274', 'HsapDv:0000158', ..., 'HsapDv:0000104', 'HsapDv:0000262', 'HsapDv:0000154', 'HsapDv:0000119', 'HsapDv:0000129']\n", - "Length: 171792\n", - "Categories (40, object): ['HsapDv:0000104', 'HsapDv:0000105', 'HsapDv:0000110', 'HsapDv:0000111', ..., 'HsapDv:0000208', 'HsapDv:0000212', 'HsapDv:0000262', 'HsapDv:0000274'] development_stage_ontology_term_id {}\n", - "array [38 24 29 ... 24 6 13] codes {}\n", - "string-array ['HsapDv:0000104' 'HsapDv:0000105' 'HsapDv:0000110' 'HsapDv:0000111'\n", - " 'HsapDv:0000112' 'HsapDv:0000115' 'HsapDv:0000119' 'HsapDv:0000120'\n", - " 'HsapDv:0000121' 'HsapDv:0000122' 'HsapDv:0000124' 'HsapDv:0000126'\n", - " 'HsapDv:0000128' 'HsapDv:0000129' 'HsapDv:0000131' 'HsapDv:0000135'\n", - " 'HsapDv:0000137' 'HsapDv:0000140' 'HsapDv:0000141' 'HsapDv:0000144'\n", - " 'HsapDv:0000145' 'HsapDv:0000147' 'HsapDv:0000148' 'HsapDv:0000152'\n", - " 'HsapDv:0000154' 'HsapDv:0000156' 'HsapDv:0000157' 'HsapDv:0000158'\n", - " 'HsapDv:0000159' 'HsapDv:0000160' 'HsapDv:0000162' 'HsapDv:0000163'\n", - " 'HsapDv:0000165' 'HsapDv:0000166' 'HsapDv:0000171' 'HsapDv:0000207'\n", - " 'HsapDv:0000208' 'HsapDv:0000212' 'HsapDv:0000262' 'HsapDv:0000274'] categories {}\n", - "categorical ['surgical resection', 'surgical resection', NaN, 'surgical resection', 'surgical resection', ..., 'surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', NaN]\n", - "Length: 171792\n", - "Categories (1, object): ['surgical resection'] sample_collection_method {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['surgical resection'] categories {}\n", - "categorical ['Baylor College of Medicine Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', NaN, 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', ..., 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', NaN]\n", - "Length: 171792\n", - "Categories (4, object): ['Baylor College of Medicine Lions Eye Bank', 'Massachusetts General Hospital', 'University of Utah', 'Utah Lions Eye Bank, Florida Lions Eye Bank'] tissue_source {}\n", - "array [ 0 3 -1 ... 0 0 -1] codes {}\n", - "string-array ['Baylor College of Medicine Lions Eye Bank'\n", - " 'Massachusetts General Hospital' 'University of Utah'\n", - " 'Utah Lions Eye Bank,\\xa0Florida Lions Eye Bank'] categories {}\n", - "categorical ['tissue', 'tissue', 'tissue', 'tissue', 'tissue', ..., 'tissue', 'tissue', 'tissue', 'tissue', 'tissue']\n", - "Length: 171792\n", - "Categories (1, object): ['tissue'] tissue_type {}\n", - "array [0 0 0 ... 0 0 0] codes {}\n", - "string-array ['tissue'] categories {}\n", - "categorical ['unknown', 'unknown', NaN, 'unknown', 'unknown', ..., 'unknown', 'unknown', 'unknown', 'unknown', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['2020', 'unknown'] sample_collection_year {}\n", - "array [ 1 1 -1 ... 1 1 -1] codes {}\n", - "string-array ['2020' 'unknown'] categories {}\n", - "categorical ['mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', ..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat...]\n", - "Length: 171792\n", - "Categories (3, object): ['mechanical dissociation,centrifugation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation'] suspension_derivation_process {}\n", - "array [2 2 1 ... 2 2 1] codes {}\n", - "string-array ['mechanical dissociation,centrifugation'\n", - " 'mechanical dissociation,detergent solubilization'\n", - " 'mechanical dissociation,enzymatic dissociation'] categories {}\n", - 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" 'f1478d8b-b0f9-4c52-908a-2a86aeadf68d'\n", - " 'fa0c4d96-399d-4cb8-a52b-974e70e0cff9'\n", - " 'fb0ffcc5-7025-4629-b0b1-a8303ecddc71'\n", - " 'fd806e8b-1a82-4b73-95c8-3db3ef1ec2c4'] categories {}\n", - "categorical ['EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', ..., 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922', 'EFO:0009922']\n", - "Length: 171792\n", - "Categories (2, object): ['EFO:0009900', 'EFO:0009922'] assay_ontology_term_id {}\n", - "array [1 1 1 ... 1 1 1] codes {}\n", - "string-array ['EFO:0009900' 'EFO:0009922'] categories {}\n", - "categorical ['3 prime tag', '3 prime tag', NaN, '3 prime tag', '3 prime tag', ..., '3 prime tag', '3 prime tag', '3 prime tag', '3 prime tag', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['3 prime tag', '5 prime tag'] sequenced_fragment {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['3 prime tag' '5 prime tag'] categories {}\n", - "categorical ['Baylor College of Medicine', 'Baylor College of Medicine', NaN, 'Baylor College of Medicine', 'Baylor College of Medicine', ..., 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', 'Baylor College of Medicine', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['Baylor College of Medicine', 'Harvard University'] institute {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['Baylor College of Medicine' 'Harvard University'] categories {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, NaN, NaN, NaN]\n", - "Length: 171792\n", - "Categories (8, object): ['SRX20898918', 'SRX20898919', 'SRX20898920', 'SRX20898921', 'SRX20898922', 'SRX20898923', 'SRX20898924', 'SRX20898925'] library_id_repository {}\n", - "array [-1 -1 -1 ... -1 -1 -1] codes {}\n", - "string-array ['SRX20898918' 'SRX20898919' 'SRX20898920' 'SRX20898921' 'SRX20898922'\n", - " 'SRX20898923' 'SRX20898924' 'SRX20898925'] categories {}\n", - "categorical ['Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', NaN, 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', ..., 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', 'Illumina NovaSeq 6000 (EFO:0008637)', NaN]\n", - "Length: 171792\n", - "Categories (1, object): ['Illumina NovaSeq 6000 (EFO:0008637)'] sequencing_platform {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['Illumina NovaSeq 6000 (EFO:0008637)'] categories {}\n", - "array [False False True ... False False True] is_primary_data {}\n", - "categorical ['CL:0000666', 'CL:0002543', 'CL:0000115', 'CL:1000414', 'CL:0000666', ..., 'CL:1000413', 'CL:1000414', 'CL:1000414', 'CL:0000666', 'CL:0000077']\n", - "Length: 171792\n", - "Categories (20, object): ['CL:0000077', 'CL:0000095', 'CL:0000097', 'CL:0000115', ..., 'CL:1000412', 'CL:1000413', 'CL:1000414', 'unknown'] cell_type_ontology_term_id {}\n", - "array [ 8 13 3 ... 18 8 0] codes {}\n", - "string-array ['CL:0000077' 'CL:0000095' 'CL:0000097' 'CL:0000115' 'CL:0000136'\n", - " 'CL:0000192' 'CL:0000235' 'CL:0000542' 'CL:0000666' 'CL:0000669'\n", - " 'CL:0000763' 'CL:0000988' 'CL:0002138' 'CL:0002543' 'CL:0002573'\n", - " 'CL:0009099' 'CL:1000412' 'CL:1000413' 'CL:1000414' 'unknown'] categories {}\n", - "categorical ['Fenestrated capillary', 'Vein', 'Endothelial Cells', 'Venule', 'Fenestrated capillary', ..., 'Arterial', 'Venule', 'Venule', 'Fenestrated capillary', 'Mesothelial Cells']\n", - "Length: 171792\n", - "Categories (21, object): ['Adipogenic Progenitors', 'Arterial', 'Arteriole', 'Endothelial Cells', ..., 'Smooth Muscle Cells', 'T/NK/B Cells', 'Vein', 'Venule'] author_cell_type {}\n", - "array [ 5 19 3 ... 20 5 11] codes {}\n", - "string-array ['Adipogenic Progenitors' 'Arterial' 'Arteriole' 'Endothelial Cells'\n", - " 'Erythroblasts - Myelocytes - Mature NK Cells' 'Fenestrated capillary'\n", - " 'Lymphatic Endothelial Cells' 'Lymphoid/B/NK Cells' 'Macrophages'\n", - " 'Mast Cells' 'Mature Adipocytes' 'Mesothelial Cells'\n", - " 'Myeloid Cells (Monocytes, Neutrophils, Macrophages)'\n", - " 'Neuronal-associated Cells' 'PRM1+ Cells' 'Pericytes' 'Schwann Cells'\n", - " 'Smooth Muscle Cells' 'T/NK/B Cells' 'Vein' 'Venule'] categories {}\n", - "categorical ['PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', ..., 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461', 'PATO:0000461']\n", - "Length: 171792\n", - "Categories (1, object): ['PATO:0000461'] disease_ontology_term_id {}\n", - "array [0 0 0 ... 0 0 0] codes {}\n", - "string-array ['PATO:0000461'] categories {}\n", - "categorical ['none', 'none', '[type 2 diabetes mellitus]', 'none', 'none', ..., 'none', 'none', 'none', 'none', 'none']\n", - "Length: 171792\n", - "Categories (3, object): ['['meningeal sarcoma']', '[type 2 diabetes mellitus]', 'none'] reported_diseases {}\n", - "array [2 2 1 ... 2 2 2] codes {}\n", - "string-array [\"['meningeal sarcoma']\" '[type 2 diabetes mellitus]' 'none'] categories {}\n", - "categorical ['PATO:0000384', 'PATO:0000383', 'PATO:0000383', 'PATO:0000383', 'PATO:0000384', ..., 'PATO:0000383', 'PATO:0000384', 'PATO:0000384', 'PATO:0000383', 'PATO:0000383']\n", - "Length: 171792\n", - "Categories (2, object): ['PATO:0000383', 'PATO:0000384'] sex_ontology_term_id {}\n", - "array [1 0 0 ... 1 0 0] codes {}\n", - "string-array ['PATO:0000383' 'PATO:0000384'] categories {}\n", - "array [ 4642. 3048. nan ... 2351. 10119. nan] nCount_RNA {}\n", - "array [1843. 1553. nan ... 1394. 3012. nan] nFeature_RNA {}\n", - "array [0.08616975 2.03412073 nan ... 0.12760527 0. nan] percent.mt {}\n", - "categorical ['Chen_lab', 'Chen_lab', NaN, 'Chen_lab', 'Chen_lab', ..., 'Chen_lab', 'Chen_lab', 'Chen_lab', 'Chen_lab', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['Chen_lab', 'Sanes_GSE236566'] Study {}\n", - "array [ 0 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['Chen_lab' 'Sanes_GSE236566'] categories {}\n", - "categorical ['Pediatric', 'Adult', NaN, 'Adult', 'Adult', ..., 'Pediatric', 'Pediatric', 'Adult', 'Adult', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['Adult', 'Pediatric'] Developmental {}\n", - "array [ 1 0 -1 ... 0 0 -1] codes {}\n", - "string-array ['Adult' 'Pediatric'] categories {}\n", - "categorical ['10h', '5h18m', NaN, '9.5h', '9h', ..., '6h30m', '10h', '6h', '8h', NaN]\n", - "Length: 171792\n", - "Categories (36, object): ['2h36m', '2h49m', '2h59m', '3h', ..., '9h', '9h10m', '10h', 'Unknown'] Post_mortemtime {}\n", - "array [34 14 -1 ... 16 26 -1] codes {}\n", - "string-array ['2h36m' '2h49m' '2h59m' '3h' '3h30m' '3h43m' '3h50m' '3h55m' '4h' '4h9m'\n", - " '4h33m' '4h48m' '5h' '5h11m' '5h18m' '5h40m' '6h' '6h2m' '6h5m' '6h17m'\n", - " '6h28m' '6h30m' '6h+' '7h' '7h26m' '7h31m' '8h' '8h1m' '8h45m' '8h50m'\n", - " '8h55m' '9.5h' '9h' '9h10m' '10h' 'Unknown'] categories {}\n", - "categorical ['10', '5.3', NaN, '9.5', '9', ..., '6.5', '10', '6', '8', NaN]\n", - "Length: 171792\n", - "Categories (36, object): ['2.6', '2.82', '2.98', '3', ..., '9.17', '10', '>6', 'Unknown'] PMT_in_hrs {}\n", - "array [33 13 -1 ... 16 25 -1] codes {}\n", - "string-array ['2.6' '2.82' '2.98' '3' '3.5' '3.72' '3.83' '3.92' '4' '4.8' '4.15'\n", - " '4.55' '5' '5.3' '5.18' '5.67' '6' '6.03' '6.5' '6.08' '6.28' '6.47' '7'\n", - " '7.43' '7.52' '8' '8.02' '8.75' '8.83' '8.92' '9' '9.5' '9.17' '10' '>6'\n", - " 'Unknown'] categories {}\n", - "categorical ['Unknown', 'OS', NaN, 'Unknown', 'Unknown', ..., 'OD', 'Unknown', 'Unknown', 'Unknown', NaN]\n", - "Length: 171792\n", - "Categories (3, object): ['OD', 'OS', 'Unknown'] Eye {}\n", - "array [ 2 1 -1 ... 2 2 -1] codes {}\n", - "string-array ['OD' 'OS' 'Unknown'] categories {}\n", - "categorical ['Peripheral', 'Peripheral', NaN, 'Macular', 'Peripheral', ..., 'Macular', 'Macular', 'Peripheral', 'Peripheral', NaN]\n", - "Length: 171792\n", - "Categories (2, object): ['Macular', 'Peripheral'] Region {}\n", - "array [ 1 1 -1 ... 1 1 -1] codes {}\n", - "string-array ['Macular' 'Peripheral'] categories {}\n", - "categorical ['3v31_BCM_1d_fetal_RPE', '3v31_MMD_23_2292_RPE', NaN, '3v31_BCM_23-1430_Mac_RPE', '3v31_BCM_22_0890_RPE', ..., '3v31_MMD_23-4291_Mac_RPE', '3v31_BCM_22-0698_Mac_RPE', '3v31_BCM_23_0313_RPE', '3v31_BCM_22_0458_RPE', NaN]\n", - "Length: 171792\n", - "Categories (82, object): ['3v31_22_0574_RPE', '3v31_22_0574_RPE_Tyto', '3v31_BCM_1d_fetal_RPE', '3v31_BCM_22-0396_Mac_RPE', ..., 'GSM7553466', 'GSM7553467', 'GSM7553469', 'GSM7553471'] sampleid {}\n", - "array [ 2 64 -1 ... 32 16 -1] codes {}\n", - "string-array ['3v31_22_0574_RPE' '3v31_22_0574_RPE_Tyto' '3v31_BCM_1d_fetal_RPE'\n", - " '3v31_BCM_22-0396_Mac_RPE' '3v31_BCM_22-0434_Mac_RPE'\n", - " '3v31_BCM_22-0698_Mac_RPE' '3v31_BCM_22-0769_Mac_RPE'\n", - " '3v31_BCM_22-0849_Mac_RPE' '3v31_BCM_22_0183_Mac_RPE'\n", - " '3v31_BCM_22_0183_RPE_WOLF' '3v31_BCM_22_0200_Mac_RPE'\n", - " '3v31_BCM_22_0200_RPE' '3v31_BCM_22_0389_RPE' '3v31_BCM_22_0396_RPE_WOLF'\n", - " '3v31_BCM_22_0434_RPE' '3v31_BCM_22_0434_RPE_WOLF' '3v31_BCM_22_0458_RPE'\n", - " '3v31_BCM_22_0500_RPE' '3v31_BCM_22_0769_RPE_WOLF'\n", - " '3v31_BCM_22_0784_Mac_RPE' '3v31_BCM_22_0784_RPE_WOLF'\n", - " '3v31_BCM_22_0849_RPE' '3v31_BCM_22_0890_RPE' '3v31_BCM_22_0896_RPE_WOLF'\n", - " '3v31_BCM_23-0131_Mac_RPE' '3v31_BCM_23-0231_Mac_RPE'\n", - " '3v31_BCM_23-0334_Mac_RPE' '3v31_BCM_23-1401_Mac_RPE'\n", - " '3v31_BCM_23-1430_Mac_RPE' '3v31_BCM_23-1448_Mac_RPE'\n", - " '3v31_BCM_23_0131_RPE' '3v31_BCM_23_0231_RPE' '3v31_BCM_23_0313_RPE'\n", - " '3v31_BCM_23_0334_RPE' '3v31_BCM_23_0358_RPE' '3v31_BCM_23_0491_RPE'\n", - " '3v31_MMD_19_D005_Mac_RPE' '3v31_MMD_19_D005_RPE'\n", - " '3v31_MMD_19_D008_Mac_RPE' '3v31_MMD_19_D008_RPE'\n", - " '3v31_MMD_22-3051_Mac_RPE' '3v31_MMD_22-3131_Mac_RPE'\n", - " '3v31_MMD_22-3991_Mac_RPE' '3v31_MMD_22-7151_Mac_RPE'\n", - " '3v31_MMD_22_1972_RPE' '3v31_MMD_22_2854_RPE' '3v31_MMD_22_3053_RPE'\n", - " '3v31_MMD_22_3132_RPE' '3v31_MMD_22_3872_RPE' '3v31_MMD_22_3952_RPE_1'\n", - " '3v31_MMD_22_3952_RPE_2' '3v31_MMD_22_3992_RPE' '3v31_MMD_22_4472_RPE'\n", - " '3v31_MMD_22_5352_RPE' '3v31_MMD_22_6392_RPE' '3v31_MMD_22_6432_RPE'\n", - " '3v31_MMD_22_7032_RPE' '3v31_MMD_22_7072_RPE' '3v31_MMD_22_7152_RPE'\n", - " '3v31_MMD_22_7432_RPE' '3v31_MMD_23-4291_Mac_RPE' '3v31_MMD_23_0194_RPE'\n", - " '3v31_MMD_23_334_RPE' '3v31_MMD_23_2252_RPE' '3v31_MMD_23_2292_RPE'\n", - " '3v31_MMD_23_3312_RPE' '3v31_MMD_23_4292_RPE' '3v31_MMD_23_5453_RPE'\n", - " '5v2_22_2854_per_RPE' '5v2_22_2854_per_RPE_spin' '10x3V31_22_0183_RPE_1'\n", - " '10x3V31_22_0183_RPE_2' '10x3V31_Adult_20_0948_Lobe_RPE'\n", - " '22_4472_per_RPE_Nu' 'GSM7553460' 'GSM7553461' 'GSM7553463' 'GSM7553464'\n", - " 'GSM7553466' 'GSM7553467' 'GSM7553469' 'GSM7553471'] categories {}\n", - "categorical ['fenestrated endothelial cell', 'vein endothelial cell', 'endothelial cell', 'endothelial cell of venule', 'fenestrated endothelial cell', ..., 'endothelial cell of artery', 'endothelial cell of venule', 'endothelial cell of venule', 'fenestrated endothelial cell', 'mesothelial cell']\n", - "Length: 171792\n", - "Categories (20, object): ['Schwann cell', 'adipocyte', 'endothelial cell', 'endothelial cell of arteriole', ..., 'pericyte', 'smooth muscle cell', 'unknown', 'vein endothelial cell'] cell_type {}\n", - "array [ 7 19 2 ... 6 7 13] codes {}\n", - "string-array ['Schwann cell' 'adipocyte' 'endothelial cell'\n", - " 'endothelial cell of arteriole' 'endothelial cell of artery'\n", - " 'endothelial cell of lymphatic vessel' 'endothelial cell of venule'\n", - " 'fenestrated endothelial cell' 'fibro/adipogenic progenitor cell'\n", - " 'hematopoietic cell' 'lymphocyte' 'macrophage' 'mast cell'\n", - " 'mesothelial cell' 'myeloid cell' 'neuron associated cell' 'pericyte'\n", - " 'smooth muscle cell' 'unknown' 'vein endothelial cell'] categories {}\n", - "categorical ['10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', ..., '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3']\n", - "Length: 171792\n", - "Categories (2, object): ['10x 5' v2', '10x 3' v3'] assay {}\n", - "array [1 1 1 ... 1 1 1] codes {}\n", - "string-array [\"10x 5' v2\" \"10x 3' v3\"] categories {}\n", - "categorical ['normal', 'normal', 'normal', 'normal', 'normal', ..., 'normal', 'normal', 'normal', 'normal', 'normal']\n", - "Length: 171792\n", - "Categories (1, object): ['normal'] disease {}\n", - "array [0 0 0 ... 0 0 0] codes {}\n", - "string-array ['normal'] categories {}\n", - "categorical ['male', 'female', 'female', 'female', 'male', ..., 'female', 'male', 'male', 'female', 'female']\n", - "Length: 171792\n", - "Categories (2, object): ['female', 'male'] sex {}\n", - "array [1 0 0 ... 1 0 0] codes {}\n", - "string-array ['female' 'male'] categories {}\n", - "categorical ['chorioretinal region', 'chorioretinal region', 'visceral abdominal adipose tissue', 'chorioretinal region', 'chorioretinal region', ..., 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'chorioretinal region', 'visceral abdominal adipose tissue']\n", - "Length: 171792\n", - "Categories (3, object): ['chorioretinal region', 'subcutaneous abdominal adipose tissue', 'visceral abdominal adipose tissue'] tissue {}\n", - "array [0 0 2 ... 0 0 2] codes {}\n", - "string-array ['chorioretinal region' 'subcutaneous abdominal adipose tissue'\n", - " 'visceral abdominal adipose tissue'] categories {}\n", - "categorical ['European', 'African American', 'European', 'African American', 'Indian', ..., 'African American', 'European', 'European', 'Hispanic or Latin American', 'African American']\n", - "Length: 171792\n", - "Categories (6, object): ['European', 'South Asian', 'Hispanic or Latin American', 'Indian', 'African American', 'unknown'] self_reported_ethnicity {}\n", - "array [0 4 0 ... 0 2 4] codes {}\n", - "string-array ['European' 'South Asian' 'Hispanic or Latin American' 'Indian'\n", - " 'African American' 'unknown'] categories {}\n", - "categorical ['newborn stage (0-28 days)', '60-year-old stage', '66-year-old stage', '90 year-old and over stage', '64-year-old stage', ..., '10-year-old stage', 'newborn stage (0-28 days)', '60-year-old stage', '25-year-old stage', '35-year-old stage']\n", - "Length: 171792\n", - "Categories (40, object): ['10-year-old stage', '11-year-old stage', '16-year-old stage', '17-year-old stage', ..., '82-year-old stage', '86-year-old stage', '90 year-old and over stage', 'newborn stage (0-28 days)'] development_stage {}\n", - "array [39 24 29 ... 24 6 13] codes {}\n", - "string-array ['10-year-old stage' '11-year-old stage' '16-year-old stage'\n", - " '17-year-old stage' '18-year-old stage' '21-year-old stage'\n", - " '25-year-old stage' '26-year-old stage' '27-year-old stage'\n", - " '28-year-old stage' '30-year-old stage' '32-year-old stage'\n", - " '34-year-old stage' '35-year-old stage' '37-year-old stage'\n", - " '41-year-old stage' '43-year-old stage' '46-year-old stage'\n", - " '47-year-old stage' '50-year-old stage' '51-year-old stage'\n", - " '53-year-old stage' '54-year-old stage' '58-year-old stage'\n", - " '60-year-old stage' '62-year-old stage' '63-year-old stage'\n", - " '64-year-old stage' '65-year-old stage' '66-year-old stage'\n", - " '68-year-old stage' '69-year-old stage' '71-year-old stage'\n", - " '72-year-old stage' '77-year-old stage' '81-year-old stage'\n", - " '82-year-old stage' '86-year-old stage' '90 year-old and over stage'\n", - " 'newborn stage (0-28 days)'] categories {}\n", - "string-array ['7jCOp<6|em' ';, 'X_umap': dask.array} obsm {}\n", - "array dask.array X_scVI {'shards': (171008, 100), 'chunks': (1024, 100), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "array dask.array X_umap {'shards': (171008, 2), 'chunks': (1024, 2), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "dict {} varm {}\n", - "dict {} obsp {}\n", - "dict {} varp {}\n", - "dict {} layers {}\n", - "dict {} uns {}\n", - "raw Raw AnnData with n_obs × n_vars = 171792 × 36406 raw {}\n", - "csr_matrix dask.array X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "csr_matrix \n", - " Coords\tValues\n", - " (0, 6381)\t0.0\n", - " (0, 7766)\t0.0\n", - " (0, 8748)\t0.0\n", - " (0, 8975)\t0.0\n", - " (0, 12475)\t0.0\n", - " (0, 12479)\t0.0\n", - " (0, 12481)\t0.0\n", - " (0, 13841)\t0.0\n", - " (0, 14274)\t0.0\n", - " (0, 14909)\t0.0\n", - " (0, 16128)\t0.0\n", - " (0, 17261)\t0.0\n", - " (0, 17271)\t0.0\n", - " (0, 17497)\t0.0\n", - " (0, 17896)\t0.0\n", - " (0, 18254)\t0.0\n", - " (0, 18515)\t0.0\n", - " (0, 18518)\t0.0\n", - " (0, 18532)\t0.0\n", - " (0, 18743)\t0.0\n", - " (0, 18745)\t0.0\n", - " (0, 18769)\t0.0\n", - " (0, 18790)\t0.0\n", - " (0, 18794)\t0.0\n", - " (0, 18807)\t0.0\n", - " :\t:\n", - " (986, 36077)\t0.0\n", - " (986, 36088)\t0.0\n", - " (986, 36101)\t0.0\n", - " (986, 36114)\t0.0\n", - " (986, 36120)\t0.0\n", - " (986, 36133)\t0.0\n", - " (986, 36140)\t0.0\n", - " (986, 36143)\t0.0\n", - " (986, 36149)\t0.0\n", - " (986, 36158)\t0.0\n", - " (986, 36179)\t0.0\n", - " (986, 36211)\t0.0\n", - " (986, 36214)\t0.0\n", - " (986, 36224)\t0.0\n", - " (986, 36244)\t0.0\n", - " (986, 36269)\t0.0\n", - " (986, 36285)\t0.0\n", - " (986, 36310)\t0.0\n", - " (986, 36318)\t0.0\n", - " (986, 36363)\t0.0\n", - " (986, 36373)\t0.0\n", - " (986, 35974)\t1.0\n", - " (986, 36296)\t1.0\n", - " (986, 36393)\t2.0\n", - " (986, 36075)\t1.0 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ + " self._set_arrayXarray(i, j, x)\n", "/home/ubuntu/home_drive/volume/arrayloaders/venv/lib/python3.12/site-packages/zarr/api/asynchronous.py:244: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.\n", " warnings.warn(\n", - "100%|██████████| 1/1 [11:12<00:00, 672.25s/it]" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "dataframe Empty DataFrame\n", - "Columns: []\n", - "Index: [ENSG00000000003, ENSG00000000005, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000000938, ENSG00000000971, ENSG00000001036, ENSG00000001084, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001561, ENSG00000001617, ENSG00000001626, ENSG00000001629, ENSG00000001630, ENSG00000001631, ENSG00000002016, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002726, ENSG00000002745, ENSG00000002746, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000002933, ENSG00000003056, ENSG00000003096, ENSG00000003137, ENSG00000003147, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003756, ENSG00000003987, ENSG00000003989, ENSG00000004059, ENSG00000004139, ENSG00000004142, ENSG00000004399, ENSG00000004455, ENSG00000004468, ENSG00000004478, ENSG00000004487, ENSG00000004534, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004776, ENSG00000004777, ENSG00000004779, ENSG00000004799, ENSG00000004809, ENSG00000004838, ENSG00000004846, ENSG00000004848, ENSG00000004864, ENSG00000004866, ENSG00000004897, ENSG00000004939, ENSG00000004948, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG00000005100, ENSG00000005102, ENSG00000005108, ENSG00000005156, ENSG00000005175, ENSG00000005187, ENSG00000005189, ENSG00000005194, ENSG00000005206, ENSG00000005238, ENSG00000005243, ENSG00000005249, ENSG00000005302, ENSG00000005339, ENSG00000005379, ENSG00000005381, ENSG00000005421, ENSG00000005436, ENSG00000005448, ENSG00000005469, ENSG00000005471, ENSG00000005483, ...]\n", - "\n", - "[36406 rows x 0 columns] var {}\n", - "string-array ['ENSG00000000003' 'ENSG00000000005' 'ENSG00000000419' ...\n", - " 'ENSG00000289604' 'ENSG00000290292' 'ENSG00000291237'] _index {}\n", - "dict {} varm {}\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "\n" + "100%|██████████| 1/1 [12:26<00:00, 746.02s/it]\n" ] } ], @@ -1298,16 +196,16 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 12, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -1352,7 +250,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -1361,7 +259,7 @@ "text": [ " 0%| | 0/171792 [00:00\n", - " Coords\tValues\n", - " (0, 6381)\t0.0\n", - " (0, 7766)\t0.0\n", - " (0, 8748)\t0.0\n", - " (0, 8975)\t0.0\n", - " (0, 12475)\t0.0\n", - " (0, 12479)\t0.0\n", - " (0, 12481)\t0.0\n", - " (0, 13841)\t0.0\n", - " (0, 14274)\t0.0\n", - " (0, 14909)\t0.0\n", - " (0, 16128)\t0.0\n", - " (0, 17261)\t0.0\n", - " (0, 17271)\t0.0\n", - " (0, 17497)\t0.0\n", - " (0, 17896)\t0.0\n", - " (0, 18254)\t0.0\n", - " (0, 18515)\t0.0\n", - " (0, 18518)\t0.0\n", - " (0, 18532)\t0.0\n", - " (0, 18743)\t0.0\n", - " (0, 18745)\t0.0\n", - " (0, 18769)\t0.0\n", - " (0, 18790)\t0.0\n", - " (0, 18794)\t0.0\n", - " (0, 18807)\t0.0\n", - " :\t:\n", - " (271248, 14024)\t3.7011654376983643\n", - " (271248, 4718)\t2.8212473392486572\n", - " (271248, 15390)\t2.8212473392486572\n", - " (271248, 4666)\t2.185926914215088\n", - " (271248, 1878)\t2.185926914215088\n", - " (271248, 5874)\t3.2066688537597656\n", - " (271248, 714)\t2.185926914215088\n", - " (271248, 8744)\t2.185926914215088\n", - " (271248, 4540)\t2.8212473392486572\n", - " (271248, 10607)\t2.185926914215088\n", - " (271248, 4525)\t2.185926914215088\n", - " (271248, 15093)\t2.185926914215088\n", - " (271248, 12417)\t2.185926914215088\n", - " (271248, 6650)\t2.185926914215088\n", - " (271248, 16129)\t2.185926914215088\n", - " (271248, 16297)\t2.185926914215088\n", - " (271248, 8169)\t2.8212473392486572\n", - " (271248, 5696)\t2.185926914215088\n", - " (271248, 8185)\t2.185926914215088\n", - " (271248, 10613)\t2.185926914215088\n", - " (271248, 10141)\t2.185926914215088\n", - " (271248, 642)\t2.185926914215088\n", - " (271248, 17141)\t2.185926914215088\n", - " (271248, 8153)\t3.4841766357421875\n", - " (271248, 4520)\t2.8212473392486572 X {'shards': (134217728,), 'chunks': (32768,), 'compressors': (BloscCodec(typesize=None, cname=, clevel=3, shuffle=, blocksize=0),)}\n", - "dataframe reference_genome \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 GRCh38 \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 GRCh38 \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 GRCh38 \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 GRCh38 \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 GRCh38 \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 GRCh38 \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 GRCh38 \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 GRCh38 \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 GRCh38 \n", - "\n", - " gene_annotation_version \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 v98 \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 v98 \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 v98 \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 v98 \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 v98 \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 v98 \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 v98 \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 v98 \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 v98 \n", - "\n", - " alignment_software \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 Cell Ranger count v7.1.0 \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 Cell Ranger count v7.1.0 \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 Cell Ranger count v7.1.0 \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 Cell Ranger count v7.1.0 \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 Cell Ranger count v7.1.0 \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 Cell Ranger count v7.1.0 \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 Cell Ranger count v7.1.0 \n", - "\n", - " intronic_reads_counted \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 yes \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 yes \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 yes \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 yes \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 yes \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 yes \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 yes \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 yes \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 yes \n", - "\n", - " donor_id donor_age \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 MMD_23_17738 10 years \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 MMD_22_20372 65 years \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 MMD_23_17738 10 years \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 BCM_22_0183 21 years \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 BCM_22_0698 1 day \n", - "... ... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 BCM_23_0491 16 years \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 BCM_22_0500 64 years \n", - "CGTAATGCAGCCGGTT-1-BOM donor-BLUE NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 MMD_22_17939 71 years \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 MMD_22_38029 82 years \n", - "\n", - " self_reported_ethnicity_ontology_term_id \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 HANCESTRO:0568 \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 HANCESTRO:0568 \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 HANCESTRO:0568 \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 HANCESTRO:0005 \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 HANCESTRO:0005 \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 HANCESTRO:0568 \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 HANCESTRO:0005 \n", - "CGTAATGCAGCCGGTT-1-BOM HANCESTRO:0568 \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 HANCESTRO:0568 \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 HANCESTRO:0014 \n", - "\n", - " donor_cause_of_death \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 unknown \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 unknown \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 unknown \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 unknown \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 unknown \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 unknown \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 unknown \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 unknown \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 unknown \n", - "\n", - " donor_living_at_sample_collection \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 False \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 False \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 False \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 False \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 False \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 False \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 False \n", - "CGTAATGCAGCCGGTT-1-BOM True \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 False \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 False \n", - "\n", - " sample_id \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 67d22e15-0d05-4c65-bda4-9cb350949266 \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 4722f3bd-2909-4026-b0b9-c471f4455658 \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 27848b53-eddb-44d6-894f-070488287fc2 \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 16565f49-122b-4ae2-93b2-c772d76fa697 \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 e322b3ae-fdee-462a-a4b3-37009212d7ed \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 46737bca-3ca2-451d-96fb-ebb433159f41 \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 8e799a46-d8e2-4e72-a483-414168d778b5 \n", - "CGTAATGCAGCCGGTT-1-BOM NaN \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 55c1fb02-40ca-462c-8578-9196e3c83f89 \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 dbe62368-43f4-41ed-a2e7-7d696b5f19d2 \n", - "\n", - " ... mapped_reference_annotation \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 ... NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 ... NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 ... NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 ... NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 ... NaN \n", - "... ... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 ... NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 ... NaN \n", - "CGTAATGCAGCCGGTT-1-BOM ... GENCODE 32 \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 ... NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 ... NaN \n", - "\n", - " sample_uuid \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM c3516e93-6857-4fb2-8eab-31038dbab88d \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " sample_derivation_process \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM dissection \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " sample_source \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM Brigham and Women's Hospital \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " donor_BMI_at_collection \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM 42.93 \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " suspension_dissociation_reagent \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM Cytoplasmic cell lysis buffer \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " suspension_dissociation_time \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM 20 minute \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " library_uuid \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM 158fa263-4d48-4894-96e2-69eba15c4c5f \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " library_starting_quantity \\\n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM 10000 nuclei \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - " leiden_scVI \n", - "3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1 NaN \n", - "3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1 NaN \n", - "3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1 NaN \n", - "3v31_BCM_22_0183_RPE_WOLF_TCCTAATTCGCGTTTC-1 NaN \n", - "3v31_BCM_22-0698_Mac_RPE_AGGGTGACATGTGTCA-1 NaN \n", - "... ... \n", - "3v31_BCM_23_0491_RPE_GAGTTGTAGATGACAT-1 NaN \n", - "3v31_BCM_22_0500_RPE_GAGGGTAGTTCAGTAC-1 NaN \n", - "CGTAATGCAGCCGGTT-1-BOM 7 \n", - "3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1 NaN \n", - "3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1 NaN \n", - "\n", - "[271249 rows x 61 columns] obs {}\n", - "string-array ['3v31_MMD_23_4292_RPE_TCAATCTAGACTACCT-1'\n", - " '3v31_MMD_22-3991_Mac_RPE_CTGCCTATCGACCTAA-1'\n", - " '3v31_MMD_23-4291_Mac_RPE_ACACCAACACTATCCC-1' ...\n", - " 'CGTAATGCAGCCGGTT-1-BOM' '3v31_MMD_23_3312_RPE_TTTCGATTCGTAGGAG-1'\n", - " '3v31_MMD_22-7151_Mac_RPE_TTGGGATTCTTGAACG-1'] _index {}\n", - "categorical ['GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', 'GRCh38', ..., 'GRCh38', 'GRCh38', NaN, 'GRCh38', 'GRCh38']\n", - "Length: 271249\n", - "Categories (1, object): ['GRCh38'] reference_genome {}\n", - "array [ 0 0 0 ... -1 0 0] codes {}\n", - "string-array ['GRCh38'] categories {}\n", - "categorical ['v98', 'v98', 'v98', 'v98', 'v98', ..., 'v98', 'v98', NaN, 'v98', 'v98']\n", - "Length: 271249\n", - "Categories (1, object): ['v98'] gene_annotation_version {}\n", - "array [ 0 0 0 ... -1 0 0] codes {}\n", - "string-array ['v98'] categories {}\n", - "categorical ['Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', ..., 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0', NaN, 'Cell Ranger count v7.1.0', 'Cell Ranger count v7.1.0']\n", - "Length: 271249\n", - "Categories (2, object): ['Cell Ranger count v7.0.1', 'Cell Ranger count v7.1.0'] alignment_software {}\n", - "array [ 1 1 1 ... -1 1 1] codes {}\n", - "string-array ['Cell Ranger count v7.0.1' 'Cell Ranger count v7.1.0'] categories {}\n", - "categorical ['yes', 'yes', 'yes', 'yes', 'yes', ..., 'yes', 'yes', NaN, 'yes', 'yes']\n", - "Length: 271249\n", - "Categories (1, object): ['yes'] intronic_reads_counted {}\n", - "array [ 0 0 0 ... -1 0 0] codes {}\n", - "string-array ['yes'] categories {}\n", - "categorical ['MMD_23_17738', 'MMD_22_20372', 'MMD_23_17738', 'BCM_22_0183', 'BCM_22_0698', ..., 'BCM_23_0491', 'BCM_22_0500', 'donor-BLUE', 'MMD_22_17939', 'MMD_22_38029']\n", - "Length: 271249\n", - "Categories (71, object): ['BCM_21_0948', 'BCM_22_0183', 'BCM_22_0200', 'BCM_22_0396', ..., 'donor-SILK', 'donor-TIME', 'donor-TREE', 'donor-ZONE'] donor_id {}\n", - "array [50 39 50 ... 53 36 46] codes {}\n", - "string-array ['BCM_21_0948' 'BCM_22_0183' 'BCM_22_0200' 'BCM_22_0396' 'BCM_22_0434'\n", - " 'BCM_22_0458' 'BCM_22_0500' 'BCM_22_0698' 'BCM_22_0769' 'BCM_22_0784'\n", - " 'BCM_22_0849' 'BCM_22_0890' 'BCM_22_0896' 'BCM_23_0131' 'BCM_23_0231'\n", - " 'BCM_23_0313' 'BCM_23_0334' 'BCM_23_0358' 'BCM_23_0491' 'BCM_23_0574'\n", - " 'BCM_23_1401' 'BCM_23_1430' 'BCM_23_1448' 'Hu13' 'Hu0218' 'Hu0220'\n", - " 'Hu0222' 'Hu0235' 'MMD_19_D005' 'MMD_19_D008' 'MMD_22_13066'\n", - " 'MMD_22_14307' 'MMD_22_16608' 'MMD_22_16860' 'MMD_22_17017'\n", - " 'MMD_22_17464' 'MMD_22_17939' 'MMD_22_20137' 'MMD_22_20357'\n", - " 'MMD_22_20372' 'MMD_22_21878' 'MMD_22_25357' 'MMD_22_33472'\n", - " 'MMD_22_34032' 'MMD_22_37089' 'MMD_22_37117' 'MMD_22_38029'\n", - " 'MMD_22_38453' 'MMD_23_01524' 'MMD_23_02177' 'MMD_23_17738'\n", - " 'MMD_23_21999' 'donor-APEX' 'donor-BLUE' 'donor-BOAT' 'donor-CORK'\n", - " 'donor-COST' 'donor-DOVE' 'donor-DOWN' 'donor-GOLD' 'donor-KEYS'\n", - " 'donor-KISS' 'donor-LACE' 'donor-OATS' 'donor-PASS' 'donor-PIKE'\n", - " 'donor-PINK' 'donor-SILK' 'donor-TIME' 'donor-TREE' 'donor-ZONE'] categories {}\n", - "categorical ['10 years', '65 years', '10 years', '21 years', '1 day', ..., '16 years', '64 years', NaN, '71 years', '82 years']\n", - "Length: 271249\n", - "Categories (31, object): ['1 day', '10 years', '11 years', '16 years', ..., '81 years', '82 years', '86 years', '>89 years'] donor_age {}\n", - "array [ 1 21 1 ... -1 24 28] codes {}\n", - "string-array ['1 day' '10 years' '11 years' '16 years' '17 years' '21 years' '25 years'\n", - " '27 years' '30 years' '32 years' '34 years' '43 years' '46 years'\n", - " '47 years' '50 years' '53 years' '58 years' '60 years' '62 years'\n", - " '63 years' '64 years' '65 years' '68 years' '69 years' '71 years'\n", - " '72 years' '77 years' '81 years' '82 years' '86 years' '>89 years'] categories {}\n", - "categorical ['HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0005', ..., 'HANCESTRO:0568', 'HANCESTRO:0005', 'HANCESTRO:0568', 'HANCESTRO:0568', 'HANCESTRO:0014']\n", - "Length: 271249\n", - "Categories (6, object): ['HANCESTRO:0005', 'HANCESTRO:0006', 'HANCESTRO:0014', 'HANCESTRO:0487', 'HANCESTRO:0568', 'unknown'] self_reported_ethnicity_ontology_term_id {}\n", - "array [4 4 4 ... 4 4 2] codes {}\n", - "string-array ['HANCESTRO:0005' 'HANCESTRO:0006' 'HANCESTRO:0014' 'HANCESTRO:0487'\n", - " 'HANCESTRO:0568' 'unknown'] categories {}\n", - "categorical ['unknown', 'unknown', 'unknown', 'unknown', 'unknown', ..., 'unknown', 'unknown', NaN, 'unknown', 'unknown']\n", - "Length: 271249\n", - "Categories (5, object): ['Coronary Artery Disease', 'Malignant Neoplasm', 'Meningeal Sarcoma', 'Septicemia', 'unknown'] donor_cause_of_death {}\n", - "array [ 4 4 4 ... -1 4 4] codes {}\n", - "string-array ['Coronary Artery Disease' 'Malignant Neoplasm' 'Meningeal Sarcoma'\n", - " 'Septicemia' 'unknown'] categories {}\n", - "categorical ['False', 'False', 'False', 'False', 'False', ..., 'False', 'False', 'True', 'False', 'False']\n", - "Length: 271249\n", - "Categories (2, object): ['False', 'True'] donor_living_at_sample_collection {}\n", - "array [0 0 0 ... 1 0 0] codes {}\n", - "string-array ['False' 'True'] categories {}\n", - "categorical ['67d22e15-0d05-4c65-bda4-9cb350949266', '4722f3bd-2909-4026-b0b9-c471f4455658', '27848b53-eddb-44d6-894f-070488287fc2', '16565f49-122b-4ae2-93b2-c772d76fa697', 'e322b3ae-fdee-462a-a4b3-37009212d7ed', ..., '46737bca-3ca2-451d-96fb-ebb433159f41', '8e799a46-d8e2-4e72-a483-414168d778b5', NaN, '55c1fb02-40ca-462c-8578-9196e3c83f89', 'dbe62368-43f4-41ed-a2e7-7d696b5f19d2']\n", - "Length: 271249\n", - "Categories (74, object): ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49', '01ffac9d-c058-47a0-969a-cb8fb51ffd03', '02be6452-fe86-4589-84a2-cbb26954a76f', '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce', ..., 'ed6fd53b-c1c3-49db-b1bb-112362a63b08', 'f86e512c-166d-41fc-b41c-b7baf70709a5', 'f768fecc-f180-420c-9b86-672ad0233e18', 'f932e7b5-1e6e-435d-8ad0-f340287da943'] sample_id {}\n", - "array [19 30 33 ... -1 17 65] codes {}\n", - "string-array ['01f33d4c-77df-4e82-b8c0-62d8c11a6e49'\n", - " '01ffac9d-c058-47a0-969a-cb8fb51ffd03'\n", - " '02be6452-fe86-4589-84a2-cbb26954a76f'\n", - " '3d67e4fc-8d51-4fa6-a4f2-50c2f433b5ce'\n", - " '5a2a6a3c-8f15-4eab-b2d1-7a6082659a83'\n", - " '5ae43655-e166-4c87-a0fd-13ee2eb525fc'\n", - " '5b839bc9-40f6-4b83-a039-2c424c917971'\n", - " '6a0b4dbd-5147-40ea-998a-3d578ae97d11'\n", - " '6fa3060a-d2b5-4cef-893f-f0b1f523ecc1'\n", - " '8e799a46-d8e2-4e72-a483-414168d778b5'\n", - " '9bc800be-b52f-485e-935b-b5bdda9fc5b8'\n", - " '12b49488-2f2d-4626-bffa-94aee3877981'\n", - " '24d12edd-fd54-4f44-9d21-63ee3c6fc807'\n", - " '25cc7497-b4b6-40e4-88ef-c0a2fe56a3ad'\n", - " '26bf8386-4a13-4fbc-8ff3-e85230a443a3'\n", - " '51e6ba30-757c-4c86-8492-16844de41645'\n", - " '54eb2056-e459-4edb-8bc8-d6adba201d61'\n", - " '55c1fb02-40ca-462c-8578-9196e3c83f89'\n", - " '64fff8e1-8db7-42e4-85df-b76ab1727414'\n", - " '67d22e15-0d05-4c65-bda4-9cb350949266'\n", - " '70df48a7-3d69-46e7-bacd-cdebc9bb6298'\n", - " '87ce0e14-0df9-4d53-99ba-9f1ebca7de9f'\n", - " '90b737c6-9ac7-4f8c-9efc-465a67874a63'\n", - " '136c4a3b-4502-4e7b-8851-fe332faf844c'\n", - " '242cabad-f81d-4fd7-8df7-fe0b318b6c34'\n", - " '245f8d19-2496-4fc0-953c-e202e74397a7'\n", - " '356c1cec-5dfc-4ed4-b07d-2f4b09dbc260'\n", - " '616d8f67-6128-4f7a-b2b3-8205f3d7d72d'\n", - " '654adbbe-18f1-42ea-944b-8aa5f5848567'\n", - " '3306e8fd-b8c5-4d15-aac1-b31daa9e86b7'\n", - " '4722f3bd-2909-4026-b0b9-c471f4455658'\n", - " '9383cb3d-f39c-48c7-b0d6-6cfc26307523'\n", - " '16565f49-122b-4ae2-93b2-c772d76fa697'\n", - " '27848b53-eddb-44d6-894f-070488287fc2'\n", - " '46737bca-3ca2-451d-96fb-ebb433159f41'\n", - " '47201e9a-732d-4bfa-9279-2dea84738e2b'\n", - " '71357c06-8ba6-4b26-bd1a-531c84a9c589'\n", - " '91523cbf-a9f1-4451-8dec-53528db17ca0'\n", - " '632242f1-c6e3-4e8e-926e-c4973fd4e695'\n", - " '717599fd-3926-428e-be6a-a959904b7c1a'\n", - " '994416c8-9bc5-4c1c-9d7c-379d4b53b573'\n", - " '4826577c-c1a3-4c38-bb75-fdce5e6bec62'\n", - " '5586185c-a422-4441-a069-8bc8c652a347'\n", - 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" 'dbe62368-43f4-41ed-a2e7-7d696b5f19d2'\n", - " 'dcdbb48e-575b-436d-a3bf-271d2625bb64'\n", - " 'dd9809d7-f120-46e6-af75-d6cdb93115ea'\n", - " 'e322b3ae-fdee-462a-a4b3-37009212d7ed'\n", - " 'e696ec77-06d7-4e17-83fa-2d97499b7e68'\n", - " 'ed6fd53b-c1c3-49db-b1bb-112362a63b08'\n", - " 'f86e512c-166d-41fc-b41c-b7baf70709a5'\n", - " 'f768fecc-f180-420c-9b86-672ad0233e18'\n", - " 'f932e7b5-1e6e-435d-8ad0-f340287da943'] categories {}\n", - "categorical ['frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', ..., 'frozen in liquid nitrogen', 'frozen in liquid nitrogen', 'flash-freezing', 'frozen in liquid nitrogen', 'frozen in liquid nitrogen']\n", - "Length: 271249\n", - "Categories (2, object): ['flash-freezing', 'frozen in liquid nitrogen'] sample_preservation_method {}\n", - "array [1 1 1 ... 0 1 1] codes {}\n", - "string-array ['flash-freezing' 'frozen in liquid nitrogen'] categories {}\n", - "categorical ['UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0019207', ..., 'UBERON:0019207', 'UBERON:0019207', 'UBERON:0014455', 'UBERON:0019207', 'UBERON:0019207']\n", - "Length: 271249\n", - "Categories (3, object): ['UBERON:0014454', 'UBERON:0014455', 'UBERON:0019207'] tissue_ontology_term_id {}\n", - "array [2 2 2 ... 1 2 2] codes {}\n", - "string-array ['UBERON:0014454' 'UBERON:0014455' 'UBERON:0019207'] categories {}\n", - "categorical ['HsapDv:0000104', 'HsapDv:0000159', 'HsapDv:0000104', 'HsapDv:0000115', 'HsapDv:0000262', ..., 'HsapDv:0000110', 'HsapDv:0000158', 'HsapDv:0000115', 'HsapDv:0000165', 'HsapDv:0000208']\n", - "Length: 271249\n", - "Categories (40, object): ['HsapDv:0000104', 'HsapDv:0000105', 'HsapDv:0000110', 'HsapDv:0000111', ..., 'HsapDv:0000208', 'HsapDv:0000212', 'HsapDv:0000262', 'HsapDv:0000274'] development_stage_ontology_term_id {}\n", - "array [ 0 28 0 ... 5 32 36] codes {}\n", - "string-array ['HsapDv:0000104' 'HsapDv:0000105' 'HsapDv:0000110' 'HsapDv:0000111'\n", - " 'HsapDv:0000112' 'HsapDv:0000115' 'HsapDv:0000119' 'HsapDv:0000120'\n", - " 'HsapDv:0000121' 'HsapDv:0000122' 'HsapDv:0000124' 'HsapDv:0000126'\n", - " 'HsapDv:0000128' 'HsapDv:0000129' 'HsapDv:0000131' 'HsapDv:0000135'\n", - " 'HsapDv:0000137' 'HsapDv:0000140' 'HsapDv:0000141' 'HsapDv:0000144'\n", - " 'HsapDv:0000145' 'HsapDv:0000147' 'HsapDv:0000148' 'HsapDv:0000152'\n", - " 'HsapDv:0000154' 'HsapDv:0000156' 'HsapDv:0000157' 'HsapDv:0000158'\n", - " 'HsapDv:0000159' 'HsapDv:0000160' 'HsapDv:0000162' 'HsapDv:0000163'\n", - " 'HsapDv:0000165' 'HsapDv:0000166' 'HsapDv:0000171' 'HsapDv:0000207'\n", - " 'HsapDv:0000208' 'HsapDv:0000212' 'HsapDv:0000262' 'HsapDv:0000274'] categories {}\n", - "categorical ['surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', 'surgical resection', ..., 'surgical resection', 'surgical resection', NaN, 'surgical resection', 'surgical resection']\n", - "Length: 271249\n", - "Categories (1, object): ['surgical resection'] sample_collection_method {}\n", - "array [ 0 0 0 ... -1 0 0] codes {}\n", - "string-array ['surgical resection'] categories {}\n", - "categorical ['Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', ..., 'Baylor College of Medicine Lions Eye Bank', 'Baylor College of Medicine Lions Eye Bank', NaN, 'Utah Lions Eye Bank, Florida Lions Eye Bank', 'Utah Lions Eye Bank, Florida Lions Eye Bank']\n", - "Length: 271249\n", - "Categories (4, object): ['Baylor College of Medicine Lions Eye Bank', 'Massachusetts General Hospital', 'University of Utah', 'Utah Lions Eye Bank, Florida Lions Eye Bank'] tissue_source {}\n", - "array [ 3 3 3 ... -1 3 3] codes {}\n", - "string-array ['Baylor College of Medicine Lions Eye Bank'\n", - " 'Massachusetts General Hospital' 'University of Utah'\n", - " 'Utah Lions Eye Bank,\\xa0Florida Lions Eye Bank'] categories {}\n", - "categorical ['tissue', 'tissue', 'tissue', 'tissue', 'tissue', ..., 'tissue', 'tissue', 'tissue', 'tissue', 'tissue']\n", - "Length: 271249\n", - "Categories (1, object): ['tissue'] tissue_type {}\n", - "array [0 0 0 ... 0 0 0] codes {}\n", - "string-array ['tissue'] categories {}\n", - "categorical ['unknown', 'unknown', 'unknown', 'unknown', 'unknown', ..., 'unknown', 'unknown', NaN, 'unknown', 'unknown']\n", - "Length: 271249\n", - "Categories (2, object): ['2020', 'unknown'] sample_collection_year {}\n", - "array [ 1 1 1 ... -1 1 1] codes {}\n", - "string-array ['2020' 'unknown'] categories {}\n", - "categorical ['mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', ..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation', 'mechanical dissociation,enzymatic dissociation']\n", - "Length: 271249\n", - "Categories (3, object): ['mechanical dissociation,centrifugation', 'mechanical dissociation,detergent solubilizat..., 'mechanical dissociation,enzymatic dissociation'] suspension_derivation_process {}\n", - "array [2 2 2 ... 1 2 2] codes {}\n", - "string-array ['mechanical dissociation,centrifugation'\n", - " 'mechanical dissociation,detergent solubilization'\n", - " 'mechanical dissociation,enzymatic dissociation'] categories {}\n", - "categorical ['c9d08907-31b1-4ae7-aeb9-4d4eddfee567', 'ebb7c928-33b8-4fc2-badf-8df6bb7055e6', 'c356b586-a9e8-446e-bbc9-78b6b71dd69a', '44511e86-169f-4143-ab8f-291d826e3dbe', '6d136144-0dcf-41a2-8cc5-fff28f1e4b05', ..., '48a85fa2-e4d9-484a-a282-4b3f7b5dda17', '42e9751f-d51d-4e32-9af4-f4734e981de5', '7a99b2a1-c3f9-4b8b-bc1a-945074b49751', '1b846b54-6cac-4ff5-b9d7-7af799f01528', '1302d1b2-5bb2-4ed1-b0d7-75ff175cc4ad']\n", - "Length: 271249\n", - "Categories (104, object): ['0bfab131-4aa6-45ba-84a7-53dfb067534d', '0d71495a-c58e-4271-be5f-ed64390d3d0e', '01b0b422-ea30-4929-bcc2-99465d5107b5', '1b8dbc8e-9586-42ba-9125-99664e094f4d', ..., 'ef3f886e-e5dd-41bf-8dfb-701dcd60cbd9', 'ef6e6788-3a53-4208-aedb-13da82d5f1bf', 'f5e609a8-4bdd-421f-92db-479d2d7b1e73', 'fce44b90-bb2b-4daa-b260-961bab432d4c'] suspension_uuid {}\n", - "array [90 99 91 ... 26 4 61] codes {}\n", - "string-array ['0bfab131-4aa6-45ba-84a7-53dfb067534d'\n", - " '0d71495a-c58e-4271-be5f-ed64390d3d0e'\n", - " '01b0b422-ea30-4929-bcc2-99465d5107b5'\n", - 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" '3v31_BCM_22_0183_RPE_WOLF' '3v31_BCM_22_0200_Mac_RPE'\n", - " '3v31_BCM_22_0200_RPE' '3v31_BCM_22_0389_RPE' '3v31_BCM_22_0396_RPE_WOLF'\n", - " '3v31_BCM_22_0434_RPE' '3v31_BCM_22_0434_RPE_WOLF' '3v31_BCM_22_0458_RPE'\n", - " '3v31_BCM_22_0500_RPE' '3v31_BCM_22_0769_RPE_WOLF'\n", - " '3v31_BCM_22_0784_Mac_RPE' '3v31_BCM_22_0784_RPE_WOLF'\n", - " '3v31_BCM_22_0849_RPE' '3v31_BCM_22_0890_RPE' '3v31_BCM_22_0896_RPE_WOLF'\n", - " '3v31_BCM_23-0131_Mac_RPE' '3v31_BCM_23-0231_Mac_RPE'\n", - " '3v31_BCM_23-0334_Mac_RPE' '3v31_BCM_23-1401_Mac_RPE'\n", - " '3v31_BCM_23-1430_Mac_RPE' '3v31_BCM_23-1448_Mac_RPE'\n", - " '3v31_BCM_23_0131_RPE' '3v31_BCM_23_0231_RPE' '3v31_BCM_23_0313_RPE'\n", - " '3v31_BCM_23_0334_RPE' '3v31_BCM_23_0358_RPE' '3v31_BCM_23_0491_RPE'\n", - " '3v31_MMD_19_D005_Mac_RPE' '3v31_MMD_19_D005_RPE'\n", - " '3v31_MMD_19_D008_Mac_RPE' '3v31_MMD_19_D008_RPE'\n", - " '3v31_MMD_22-3051_Mac_RPE' '3v31_MMD_22-3131_Mac_RPE'\n", - " '3v31_MMD_22-3991_Mac_RPE' '3v31_MMD_22-7151_Mac_RPE'\n", - " '3v31_MMD_22_1972_RPE' '3v31_MMD_22_2854_RPE' '3v31_MMD_22_3053_RPE'\n", - " '3v31_MMD_22_3132_RPE' '3v31_MMD_22_3872_RPE' '3v31_MMD_22_3952_RPE_1'\n", - " '3v31_MMD_22_3952_RPE_2' '3v31_MMD_22_3992_RPE' '3v31_MMD_22_4472_RPE'\n", - " '3v31_MMD_22_5352_RPE' '3v31_MMD_22_6392_RPE' '3v31_MMD_22_6432_RPE'\n", - " '3v31_MMD_22_7032_RPE' '3v31_MMD_22_7072_RPE' '3v31_MMD_22_7152_RPE'\n", - " '3v31_MMD_22_7432_RPE' '3v31_MMD_23-4291_Mac_RPE' '3v31_MMD_23_0194_RPE'\n", - " '3v31_MMD_23_334_RPE' '3v31_MMD_23_2252_RPE' '3v31_MMD_23_2292_RPE'\n", - " '3v31_MMD_23_3312_RPE' '3v31_MMD_23_4292_RPE' '3v31_MMD_23_5453_RPE'\n", - " '5v2_22_2854_per_RPE' '5v2_22_2854_per_RPE_spin' '10x3V31_22_0183_RPE_1'\n", - " '10x3V31_22_0183_RPE_2' '10x3V31_Adult_20_0948_Lobe_RPE'\n", - " '22_4472_per_RPE_Nu' 'GSM7553460' 'GSM7553461' 'GSM7553463' 'GSM7553464'\n", - " 'GSM7553466' 'GSM7553467' 'GSM7553469' 'GSM7553471'] categories {}\n", - "categorical ['endothelial cell of venule', 'endothelial cell of venule', 'fenestrated endothelial cell', 'endothelial cell of venule', 'endothelial cell of venule', ..., 'fenestrated endothelial cell', 'fenestrated endothelial cell', 'mesothelial cell', 'fenestrated endothelial cell', 'endothelial cell of venule']\n", - "Length: 271249\n", - "Categories (20, object): ['Schwann cell', 'adipocyte', 'endothelial cell', 'endothelial cell of arteriole', ..., 'pericyte', 'smooth muscle cell', 'unknown', 'vein endothelial cell'] cell_type {}\n", - "array [ 6 6 7 ... 13 7 6] codes {}\n", - "string-array ['Schwann cell' 'adipocyte' 'endothelial cell'\n", - " 'endothelial cell of arteriole' 'endothelial cell of artery'\n", - " 'endothelial cell of lymphatic vessel' 'endothelial cell of venule'\n", - " 'fenestrated endothelial cell' 'fibro/adipogenic progenitor cell'\n", - " 'hematopoietic cell' 'lymphocyte' 'macrophage' 'mast cell'\n", - " 'mesothelial cell' 'myeloid cell' 'neuron associated cell' 'pericyte'\n", - " 'smooth muscle cell' 'unknown' 'vein endothelial cell'] categories {}\n", - "categorical ['10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', ..., '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3', '10x 3' v3']\n", - "Length: 271249\n", - "Categories (2, object): ['10x 5' v2', '10x 3' v3'] assay {}\n", - 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"Categories (40, object): ['10-year-old stage', '11-year-old stage', '16-year-old stage', '17-year-old stage', ..., '82-year-old stage', '86-year-old stage', '90 year-old and over stage', 'newborn stage (0-28 days)'] development_stage {}\n", - "array [ 0 28 0 ... 5 32 36] codes {}\n", - "string-array ['10-year-old stage' '11-year-old stage' '16-year-old stage'\n", - " '17-year-old stage' '18-year-old stage' '21-year-old stage'\n", - " '25-year-old stage' '26-year-old stage' '27-year-old stage'\n", - " '28-year-old stage' '30-year-old stage' '32-year-old stage'\n", - " '34-year-old stage' '35-year-old stage' '37-year-old stage'\n", - " '41-year-old stage' '43-year-old stage' '46-year-old stage'\n", - " '47-year-old stage' '50-year-old stage' '51-year-old stage'\n", - " '53-year-old stage' '54-year-old stage' '58-year-old stage'\n", - " '60-year-old stage' '62-year-old stage' '63-year-old stage'\n", - " '64-year-old stage' '65-year-old stage' '66-year-old stage'\n", - " '68-year-old stage' '69-year-old stage' '71-year-old stage'\n", - " '72-year-old stage' '77-year-old stage' '81-year-old stage'\n", - " '82-year-old stage' '86-year-old stage' '90 year-old and over stage'\n", - " 'newborn stage (0-28 days)'] categories {}\n", - "string-array ['WvwV68V!*6' 'VDY0p`o_;k' 'RT8u$f3J6y' ... 'ug{*mFhqtP' '((KWHh!1^H'\n", - " 'kesisG#am%'] observation_joinid {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'GENCODE 32', NaN, NaN]\n", - "Length: 271249\n", - "Categories (1, object): ['GENCODE 32'] mapped_reference_annotation {}\n", - "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", - "string-array ['GENCODE 32'] categories {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'c3516e93-6857-4fb2-8eab-31038dbab88d', NaN, NaN]\n", - "Length: 271249\n", - "Categories (22, object): ['0a5ca5af-a3ba-4f57-a692-c1c585051aec', '1fc35617-2b40-498b-9060-4f0a911ae941', '3adc1917-d13f-47ed-a76d-361cd6d2c790', '07c898fe-dc65-4550-b68e-967fc10861cf', ..., 'e1abc275-33f0-4198-8b08-c71f82d1fbd6', 'e4fd6c96-fbde-46a4-a749-368dbd372dab', 'ee2af55d-a295-4b3f-8f2e-3b95d3d62a22', 'f3668d06-5641-4ba5-bcbe-d18a7bb9b4e7'] sample_uuid {}\n", - "array [-1 -1 -1 ... 13 -1 -1] codes {}\n", - "string-array ['0a5ca5af-a3ba-4f57-a692-c1c585051aec'\n", - " '1fc35617-2b40-498b-9060-4f0a911ae941'\n", - 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"Length: 271249\n", - "Categories (1, object): ['dissection'] sample_derivation_process {}\n", - "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", - "string-array ['dissection'] categories {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'Brigham and Women's Hospital', NaN, NaN]\n", - "Length: 271249\n", - "Categories (1, object): ['Brigham and Women's Hospital'] sample_source {}\n", - "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", - "string-array [\"Brigham and Women's Hospital\"] categories {}\n", - "array [ nan nan nan ... 42.93 nan nan] donor_BMI_at_collection {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, 'Cytoplasmic cell lysis buffer', NaN, NaN]\n", - "Length: 271249\n", - "Categories (1, object): ['Cytoplasmic cell lysis buffer'] suspension_dissociation_reagent {}\n", - "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", - "string-array ['Cytoplasmic cell lysis buffer'] categories {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, '20 minute', NaN, NaN]\n", - "Length: 271249\n", - "Categories (1, object): ['20 minute'] suspension_dissociation_time {}\n", - "array [-1 -1 -1 ... 0 -1 -1] codes {}\n", - "string-array ['20 minute'] categories {}\n", - "categorical [NaN, NaN, NaN, NaN, NaN, ..., NaN, NaN, '158fa263-4d48-4894-96e2-69eba15c4c5f', NaN, NaN]\n", - "Length: 271249\n", - "Categories (22, object): ['0eb623da-699f-4cf9-8c1f-d610b6898c53', '1e290323-810e-4202-9da8-097a90553768', '3df6c15b-fc26-437f-820f-0ec3a771990f', '4b9e7151-7395-4b1f-8c9b-2033f6658a54', ..., '90113f89-09cc-49e6-9792-1df25602e7ad', '20027346-e846-46db-91c7-0574419aedda', 'a3855ec2-6539-42e0-b663-3af74aec8b81', 'bb10ba9e-5405-46f7-bf85-f1eb11467574'] library_uuid {}\n", - "array [-1 -1 -1 ... 15 -1 -1] codes {}\n", - "string-array ['0eb623da-699f-4cf9-8c1f-d610b6898c53'\n", - " '1e290323-810e-4202-9da8-097a90553768'\n", - " '3df6c15b-fc26-437f-820f-0ec3a771990f'\n", - " '4b9e7151-7395-4b1f-8c9b-2033f6658a54'\n", - " '4c67c43b-e36c-4efc-8469-cd9619280c98'\n", - " '5a8f2276-f6f4-4e79-868d-636fdefbb347'\n", - 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}, - { - "name": "stderr", - "output_type": "stream", - "text": [ + " utils.warn_names_duplicates(\"obs\")\n", "/home/ubuntu/home_drive/volume/arrayloaders/venv/lib/python3.12/site-packages/zarr/api/asynchronous.py:244: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.\n", " warnings.warn(\n", - "100%|██████████| 1/1 [00:40<00:00, 40.62s/it]" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "dataframe Empty DataFrame\n", - "Columns: []\n", - "Index: [ENSG00000000003, ENSG00000000005, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000000938, ENSG00000000971, ENSG00000001036, ENSG00000001084, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001561, ENSG00000001617, ENSG00000001626, ENSG00000001629, ENSG00000001630, ENSG00000001631, ENSG00000002016, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002726, ENSG00000002745, ENSG00000002746, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000002933, ENSG00000003056, ENSG00000003096, ENSG00000003137, ENSG00000003147, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003756, ENSG00000003987, ENSG00000003989, ENSG00000004059, ENSG00000004139, ENSG00000004142, ENSG00000004399, ENSG00000004455, ENSG00000004468, ENSG00000004478, ENSG00000004487, ENSG00000004534, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004776, ENSG00000004777, ENSG00000004779, ENSG00000004799, ENSG00000004809, ENSG00000004838, ENSG00000004846, ENSG00000004848, ENSG00000004864, ENSG00000004866, ENSG00000004897, ENSG00000004939, ENSG00000004948, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG00000005100, ENSG00000005102, ENSG00000005108, ENSG00000005156, ENSG00000005175, ENSG00000005187, ENSG00000005189, ENSG00000005194, ENSG00000005206, ENSG00000005238, ENSG00000005243, ENSG00000005249, ENSG00000005302, ENSG00000005339, ENSG00000005379, ENSG00000005381, ENSG00000005421, ENSG00000005436, ENSG00000005448, ENSG00000005469, ENSG00000005471, ENSG00000005483, ...]\n", - "\n", - "[36406 rows x 0 columns] var {}\n", - "string-array ['ENSG00000000003' 'ENSG00000000005' 'ENSG00000000419' ...\n", - " 'ENSG00000289604' 'ENSG00000290292' 'ENSG00000291237'] _index {}\n", - "dict {} varm {}\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "\n" + "100%|██████████| 1/1 [00:30<00:00, 30.76s/it]\n" ] } ],