cellAdmix-Notebooks

To install the dependencies, run these commands from the project root:

BiocManager::install("sva")

Rscript -e "devtools::install_deps()"

To create the necessary data folders, run:

Rscript -e "dataorganizer::CreateFolders()"

Notebooks

The notebooks are organized by dataset in the Analyses folder. Within each dataset folder, numbered notebooks should be run first in the order of the numbers. Non-numbered notebooks can be run in any order after the numbered ones.

Data

The notebooks assume that the data is stored in ./data/spatial_data. See R/data_loading.R for details.

This section explains how to download and prepare the data required for the notebooks.

To download the data, use the following links:

• Human Breast Cancer (BC)
  • Xenium: 10x Genomics Preview. Only need 'In Situ Sample 1, Replicate 1', 'Xenium Output Bundle', which should be unzipped into the root dataset folder.
  • scRNA-seq: GEO GSM7782698. Need GSM7782698_count_raw_feature_bc_matrix.h5 (from GEO) and umap_annotation.csv from Source Data -> "Fig. 3E".
• Mouse Hypothalamus (Brain)
  • MERFISH: Dryad
  • scRNA-seq: GEO GSE113576. Only need regional_sampling_UMIcounts.txt and mouse_int_meta.csv files.
  • scRNA-seq metadata from the paper supplementary Table 1 should be saved in mouse_hypothalamus_rna/scRNA_metadata.xlsx.
  • There is also merfish_barcodes.csv with the molecule information, which wasn't published in the original study.
• Mouse Ileum (Gut)
  • MERFISH: Dryad
  • scRNA-seq: GEO GSE92332
• Human NSCLC (NSCLC)
  • CosMx: Nanostring FFPE.
  • scRNA-seq: GEO GSE127465
  • DIALOGUE results: GitHub. Put DIALOGUE1_LungCancer.SMI.rds in NSCLC/CosmX.
  • iTALK LR database: GitHub. Put LR_database.rda in NSCLC/CosmX.
• Human Ovarian Cancer (OC)
  • Xenium: 10x Genomics
  • scRNA-seq: 10x Genomics scFFPE
• Human Pancreatic Cancer (Pancreas)
  • Xenium: 10x Genomics
  • snRNA-seq: Single Cell Portal

The code assumes that the data is stored in ../data with a separate subfolder per dataset and per modality. See data_mapping.yml for details. There, you can also change the paths to match your local setup.