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

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katsikora opened this issue Feb 20, 2024 · 2 comments
Open
1 of 6 tasks

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

katsikora opened this issue Feb 20, 2024 · 2 comments
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ATAC-seq ChIP-Seq enhancement RNA-seq WGBS

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@katsikora
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katsikora commented Feb 20, 2024 •
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  • mRNAseq DESeq2
  • mRNAseq sleuth
  • noncoding RNAseq
  • WGBS
  • ATAC-seq
  • ChIP-seq
@katsikora katsikora changed the title add support for custom model formula and contrast to mRNAseq and other workflows add support for custom model formula to mRNAseq and other workflows Feb 20, 2024
@sunta3iouxos
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could you please also add batch effect?

@katsikora
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@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.

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@katsikora @sunta3iouxos