Normalization of RNA-seq gene expression.
Project description
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 rnanormSee rnanorm command help:
rnanorm --helpRun rnanorm with pre-computed gene lengths:
rnanorm expr.tsv --cpm-output=expr.cpm.tsv --tpm-output=expr.tpm.tsv --gene-lengths=lengths.tsvRun 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.gtfContributing
Install rnanorm Python package for development:
flit install --deps=all --symlinkRun all tests and linters:
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