modules/deseq2_differential
runs a differential expression analysis with DESeq2
Input
Groovy Map containing contrast information. This can be used at the
workflow level to pass optional parameters to the module, e.g.
[ id:‘contrast1’, blocking:‘patient’ ] passed in as ext.args like:
‘—blocking_variable $meta.blocking’.
The column in the sample sheet that should be used to define groups for
comparison
The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples
The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples
Output
TSV-format table of differential expression information as output by DESeq2
deseq2.results.tsv Optional, TSV-format counts matrix, normalised to size factors, with
variance stabilisation applied via rlog().
rlog.tsv Optional, TSV-format counts matrix, normalised to size factors, with
variance stabilisation applied via vst().
vst_counts.tsv included in
maintainer
