.gitignore

@@ -2,6 +2,7 @@
 00_RawData
 01_Reference
 02_Container/cellranger.sif
+02_Container/mambaforge:23.1.0-1.sif
 05_Output
 .vscode/
 .bash_history/
@@ -12,4 +13,13 @@
 .local/
 .singularity/
 snakemake_virtenv/
-
+test
+S004647_to_S004650_unoptimized_ref/
+S004647_to_S004650/
+__pycache__
+.netrc
+global_report.html
+run_slurm_sims.sh
+run_slurm.sh
+run-slurm_sims_gpu.sh
+processing_multiplex.Rmd_all

02_Container/ReferenceEnhancer.yaml

@@ -0,0 +1,14 @@
+channels:
+    - bioconda
+    - conda-forge
+    - defaults
+    - r
+dependencies:
+    - r-devtools=2.4.5
+    - bedops
+    - bedtools
+    - bioconda::bioconductor-rtracklayer
+    - bioconda::bioconductor-rsamtools
+    - bioconda::bioconductor-iranges
+    - bioconda::bioconductor-genomicranges
+    - bioconda::bioconductor-genomicalignments

02_Container/dotplot.yaml

@@ -0,0 +1,9 @@
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.9  # Replace with your preferred Python version
+  - numpy
+  - pandas
+  - matplotlib
+  - scikit-image

02_Container/eval_prediction.yaml

@@ -0,0 +1,10 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    - r-base = 4.3.2
+    - r-data.table = 1.14.10
+    - r-ggplot2
+    - r-dplyr

02_Container/fastqc.yaml

@@ -0,0 +1,4 @@
+channels:
+    - bioconda
+dependencies:
+    - fastqc=0.12.1

02_Container/knnor.yaml

@@ -0,0 +1,12 @@
+channels :
+    - main
+    - defaults
+    - bioconda
+    - conda-forge
+dependencies :
+    - python = 3.9
+    - pandas
+    - numpy
+    - pip
+    - pip :
+        - knnor

02_Container/merge.yaml

@@ -0,0 +1,9 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    - r-base
+    - r-seurat =4.0.3
+    - r-sessioninfo =1.2.1

02_Container/multiqc.yaml

@@ -1,7 +1,7 @@
 channels:
-  - bioconda
-  - conda-forge
-  - defaults
-  - r
+    - bioconda
+    - conda-forge
+    - defaults
+    - r
 dependencies:
-  - multiqc=1.11
+    - bioconda::multiqc=1.14

02_Container/normalisation.yaml

@@ -0,0 +1,16 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    - r-base = 4.3.2
+    - r-biocmanager = 1.30.22
+    - bioconductor-singlecellexperiment = 1.24.0
+    - r-magick = 2.7.5
+    - bioconductor-scran = 1.30.0
+    - r-data.table = 1.14.10
+    - r-matrix = 1.6.1
+    - r-irlba = 2.3.5.1
+    - bioconductor-scater = 1.30.1
+    - r-seurat = 4.4.0

02_Container/preparation_sims.yaml

@@ -0,0 +1,21 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    - r-base = 4.3.2
+    - r-biocmanager = 1.30.22
+    # - bioconductor-singlecellexperiment=1.22.0
+    - bioconductor-singlecellexperiment = 1.24.0
+    - r-magick = 2.7.5
+    - bioconductor-scran = 1.30.0
+    - r-data.table = 1.14.10
+    - r-matrix = 1.6.1
+    - r-irlba = 2.3.5.1
+    - conda-forge::anndata = 0.9.2
+    - conda-forge::pandas = 2.1.1
+    - bioconductor-scater = 1.30.1
+    - r-seurat = 4.4.0
+    - bioconductor-zellkonverter = 1.12.1
+    - bioconductor-singlecelltk = 2.12.0

02_Container/processing_multiplex.yaml

@@ -0,0 +1,36 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    # DropletUtils
+    - bioconductor-dropletutils = 1.10.3
+    - r-cowplot = 1.1.1
+    - r-matrix = 1.4-1
+    - bioconductor-beachmat = 2.6.4
+    - bioconductor-biocparallel
+    # Seurat
+    - r-ggplot2 = 3.3.6
+    - r-dt = 0.25
+    - r-data.table = 1.14.2
+    - r-seurat = 4.1.1
+    - r-dplyr = 1.0.10
+    - r-patchwork = 1.1.2
+    - bioconductor-glmgampoi = 1.2.0
+    - r-devtools = 2.4.4
+    - r-sessioninfo = 1.2.2
+    - bioconductor-dittoseq = 1.2.5
+    - bioconductor-enhancedvolcano
+    - r-ggpubr = 0.4.0
+    # Report snakemake
+    - conda-forge::jinja2=2.11.2
+    - conda-forge::networkx=2.5
+    - conda-forge::pygraphviz=1.6
+    - conda-forge::pygments=2.7.2
+    # For visualizing workflows
+    - graphviz=2.42.3
+    - xorg-libxrender
+    - xorg-libxpm
+    - conda-forge::r-rmarkdown=2.5
+    - conda-forge::r-tidyverse=1.3.0

02_Container/rm_doublets.yaml

@@ -0,0 +1,24 @@
+channels :
+    - r
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies :
+    - r-base
+    - bioconductor-scran = 1.10.1
+    # - r-biocmanager
+    # - r-seurat = 3.1.5 
+    - r-irlba = 2.3.3
+    - bioconductor-singlecellexperiment = 1.4.0
+    # - bioconductor-biocparallel
+    # - r-ggplot2
+    - r-matrix = 1.2-18 
+    # - r-matrixstats
+    # - r-igraph
+    - bioconductor-scater = 1.10.1
+    - r-reshape2 = 1.4.4
+    - r-knitr = 1.28
+    - conda-forge::r-rmarkdown = 2.1 
+    - bioconductor-biomart = 2.38.0 
+    # - r-data.table
+    # - r-seuratobject

02_Container/seurat.yaml

@@ -4,16 +4,19 @@ channels :
     - conda-forge
     - defaults
 dependencies :
-    - r-ggplot2 =3.3.5
+    - r-ggplot2
+    - r-dt
     - r-data.table =1.14.2
     - r-seurat =4.0.3
-    - r-dplyr =1.0.7
+    - r-dplyr =1.0.9
     - r-patchwork =1.1.1
     - bioconductor-glmgampoi =1.2.0
     - r-devtools =2.4.2
     - r-sessioninfo =1.2.1
     - bioconductor-dittoseq
     - bioconductor-enhancedvolcano=1.8.0
+    - r-ggpubr
+    - r-cowplot
     # Report snakemake
     - conda-forge::jinja2=2.11.2
     - conda-forge::networkx=2.5

02_Container/sims.yaml

@@ -0,0 +1,14 @@
+channels :
+  - main
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies : 
+  - python = 3.9
+  - bioconductor-zellkonverter = 1.12.1
+  - pip
+  - pip:
+    - --upgrade pip setuptools wheel
+    # - --install tensorflow-gpu
+    # Sims version Mar 14, 2024
+    - --use-pep517 git+https://github.com/braingeneers/SIMS.git@fb652b8822636da039324e659f1b114b9d257fa2