Merge pull request #5 from metavannier/SRP287614

Srp287614

Author: metavannier

03_Script/diffexp_subset.Rmd

@@ -37,7 +37,7 @@ library(EnhancedVolcano)
 read_chunk( path=file.path( SCRIPTDIR, "diffexp_subset.R"))
 ```
 
-## Differential epression of marker genes inside cluster
+## Differential expression of marker genes inside cluster
 
 We remove NFAT2C and PAX5 from the analyse because they are not in the count matrix. Maybe they have an other name or they don't pass the filter (present in x cells etc...).
 We select cluster of cells with more than 5 cells with an expression of `r snakemake@params[["markergene"]]`. 

README.md

@@ -11,6 +11,12 @@ Thomas Vannier (@metavannier), https://centuri-livingsystems.org/t-vannier/
 This workflow performs a Snakemake pipeline to process 10x single-cell RNAseq data from fastq files to the analysis of the differential expression of marker-genes.
 Correction for technical differences between datasets can be included (i.e. batch effect correction) with the integration method during the sctransform process in Seurat to perform comparative scRNA-seq analysis across experimental conditions.
 
+Steps for the analysis:
+- cellranger.smk: Build the reference, count and aggregate with [cellranger v6.0.0](docker://litd/docker-cellranger).
+- seurat.smk: Run [seurat v4.0.3](https://www.cell.com/cell/fulltext/S0092-8674(21)00583-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421005833%3Fshowall%3Dtrue) for the clustering.
+- differential_exp.smk: Differential expression based on the non-parametric Wilcoxon rank sum test. DE testing is performed on measured data.
+- diffexp_subset.smk: Differential expression analyses inside cluster after a subset on the marker gene expression.
+
 ## Usage
 
 You need to install [Singularity](https://github.com/hpcng/singularity/blob/master/INSTALL.md#install-golang) on your computer. This workflow also work in a slurm environment.
@@ -48,7 +54,7 @@ Configure the workflow according to your needs via editing the files and reposit
 
 - Then execute the workflow locally via
 
-`snakemake  --use-conda --use-singularity --cores 10`
+`snakemake --use-conda --use-singularity --cores 10`
 
 #### On a cluster