Output files for differentially expressed genes

ktrns / scrnaseq

Workflow for single-cell RNA-seq analysis using Seurat

MIT License

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Output files for differentially expressed genes #80

Closed ktrns closed 3 years ago

ktrns commented 3 years ago

Contrasts: Can we have ONE file with one tab per contrast? (as we have one tab per cluster for marker genes)

Functions: I'd prefer if we only write files if there is something to write, i.e. there are enriched functions and so on... In my current report, there are no enrichments, but a tab called "All" with only the headers.

andpet0101 commented 3 years ago

Regarding the contrasts: What do you do with subsets? No I think one file per contrast is good especially since contrasts may be separate analyses.

Functions: Maybe but on the other hand I think that an empty table is more informative - it tells you that there were no DEGs. A missing file could be interpreted as a bug.