add support for custom model formula to mRNAseq and other workflows

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

http://snakepipes.readthedocs.io

389 stars 88 forks source link

add support for custom model formula to mRNAseq and other workflows #988

Open katsikora opened 9 months ago

katsikora commented 9 months ago

[x] mRNAseq DESeq2
[ ] mRNAseq sleuth
[ ] noncoding RNAseq
[ ] WGBS
[ ] ATAC-seq
[ ] ChIP-seq

sunta3iouxos commented 7 months ago

could you please also add batch effect?

katsikora commented 7 months ago

@sunta3iouxos what do you mean with that? We already have support for modeling batch effect if you add it as a column between "name" and "condition" in your sample sheet. Then it will be automatically added to the model. Custom formula will allow for using e.g. only some columns that are between "name" and "condition" in the sample sheet (by default, all columns are used), as well as interaction terms.