Scripts for scRNA-seq pipeline
All scripts can be found in /fsx/home/abdalla/pipelineRMD
Important metadata files to have examples:
groups.csv:
sample,donor,group
CSC000084,O,DMSO_Unstim_0_24.5
CSC000085,O,MOL-00010082-005_Unstim_5_24.5
CSC000086,O,MOL-00010255-005_Unstim_5_24.5
contrasts.csv
MOL-00010082-005_Unstim_5_24.5,DMSO_Unstim_0_24.5
MOL-00010255-005_Unstim_5_24.5,DMSO_Unstim_0_24.5
MOL-00010082-005_R848_5_24.5,DMSO_R848_0_24.5
scRNA_QCperSample.R: Runs the QC per sample and saves an rds file
Example: Rscript /fsx/home/abdalla/pipelineRMD/scRNA_QCperSample.R cellrangerout/CSC000084/outs/filtered_feature_bc_matrix.h5 /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/groups.csv Human /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/sampleRDS pbmcref Immune_All_Low.pkl
scQC_merge.R: merges the per sample RDS files saved in sampleRDS, saves a merged seurat object "filtered.rds" that has clusters,UMAP and annotations
Example: Rscript /fsx/home/abdalla/pipelineRMD/scQC_merge.R /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/sampleRDS /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/merged.html
annot.R: Run annotation report with different methods
Example: /fsx/home/abdalla/pipelineRMD/pipelineAnnot.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmcAnnot.html
compareComposition.R: Compares the composition (number of cells per annotation) per group
Example: /fsx/home/abdalla/pipelineRMD/compareComposition.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmcAnnot.html
scDE.R Runs DE and GSEA/Enrichment per using pseudobulk per group per contrast
Example: Rscript /fsx/home/abdalla/pipelineRMD/scDE.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmcDE.html
DE_donor.R: Runs DE per donor
Example:
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 S /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ultima_DE_S.html
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 O /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ultima_DE_O.html
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 Y /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ultima_DE_Y.html
DE_donor_enrich.R Runs GSEA/Enrichment per donor
Example:
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor_enrich.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 S /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmc2_enrich_S.html
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor_enrich.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 O /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmc2_enrich_O.html
Rscript /fsx/home/abdalla/pipelineRMD/DE_donor_enrich.R filtered.rds /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/ predicted.celltype.l2 Y /fsx/home/abdalla/pbmc_scRNA_TKT00078/output/pbmc2_enrich_Y.html
compare_donor_DE.R: Compared the DE results per donor input needs to the DE results folder per donor /fsx/home/abdalla/pipelineRMD/compare_donor_DE.R donorDE_predicted.celltype.l2/ /fsx/home/abdalla/ultima_Compare/output/ compareDonors.html