rnanorm 1.3.0

Normalization of RNA-seq gene expression.

Normalization of RNA-seq gene expression. Supported methods: Transcript per kilobase million (TPM) and Counts per million (CPM).

Usage

Install rnanorm Python package:

pip install rnanorm

See rnanorm command help:

rnanorm --help

Run rnanorm with pre-computed gene lengths:

rnanorm expr.tsv --cpm-output=expr.cpm.tsv --tpm-output=expr.tpm.tsv --gene-lengths=lengths.tsv

Run rnanorm with genome annotation - gene lengths will be computed on the fly:

rnanorm expr.tsv --cpm-output=expr.cpm.tsv --tpm-output=expr.tpm.tsv --annotation=annot.gtf

Contributing

Install rnanorm Python package for development:

flit install --deps=all --symlink

Run all tests and linters:

tox