Normalization of RNA-seq gene expression.

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  • License: Apache Software License
  • Author: Genialis, Inc.
  • Requires: Python >=3.6, <3.9
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Build Status Code Style Black Version on PyPI Supported Python versions Number of downloads from PyPI

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

Project details

Verified details

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Avatar for acopar from gravatar.com acopar Avatar for dblenkus from gravatar.com dblenkus Avatar for genialis-bot from gravatar.com genialis-bot

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Project links
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  • License: Apache Software License
  • Author: Genialis, Inc.
  • Requires: Python >=3.6, <3.9
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2.1.0

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1.3.0

1.2.1

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