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Description
For integrating BioQC in automated workflows (such as nfcore/rnaseq) it would be really helpful to have a CLI to BioQC.
Essentially, the script should take
- a gene expression matrix
- optionally, a GMT file, or just use BioQC's default if none is specified
- optionally, a species identifier to automatically remap to orthologous gene symbols (maybe even autodetect that for rat and mouse)
and produce
- A heatmap with all signatures that are detected in at least one sample
- A CSV/TSV file with all signature scores
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