rnanorm 1.3.1

Normalization of RNA-seq gene expression.

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

The TPM normalization can either accept pre-computed gene lengths on the input or compute gene lengths from gene annotation in GTF format, using the union exon-based approach. The computed gene lengths are identical to the lengths reported by featureCounts (validated for Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta of ENSEMBL and UCSC annotations).

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