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Update docs/output.md
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Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
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rezaeinfo and pinin4fjords committed Mar 20, 2024
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Expand Up @@ -76,7 +76,6 @@ Most plots are included in the HTML report (see above), but are also included in

- `[contrast_name].[deseq2|limma].results.tsv`: Results of DESeq2 differential analyis (RNA-seq) OR limma differential analysis (Affymetrix arrays, GEO studies, Maxquant proteomics studies)
- `[contrast_name].[deseq2|limma].results_filtered.tsv`: Results of DESeq2 differential analyis (RNA-seq) OR limma differential analysis (Affymetrix arrays, GEO studies, Maxquant proteomics studies); filtered for differentially abundant entries

- `gsea/`: Directory containing tables of differential gene set analyis from GSEA (where enabled)

- `[contrast]/[contrast].gsea_report_for_[condition].tsv`: A GSEA report table for each side of each contrast
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