Differential gene expression analysis and pathway analysis of RNAseq data
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Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden #215
Boxplots are now generated not from raw, but from transformed counts. If batcheffect, will plot them before and after transformation. The plot titles and filenames now also contain their genenames in addition to the geneIDs. Also, in the PCA label plots, the threshold for hiding overlapping labels has been increased
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/rnadeseq branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
Boxplots are now generated not from raw, but from transformed counts. If batcheffect, will plot them before and after transformation. The plot titles and filenames now also contain their genenames in addition to the geneIDs. Also, in the PCA label plots, the threshold for hiding overlapping labels has been increased
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).