HTSeq

DEVS: https://github.com/htseq/htseq

DOCS: https://htseq.readthedocs.io

A Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. A popular use of HTSeq is htseq-count, a tool to quantify gene expression in RNA-Seq and similar experiments.

Requirements

To use HTSeq you will need:

• Python >= 3.6 (note: Python 2.7 support has been dropped)
• numpy
• pysam

To run the htseq-qa script, you will also need:

• matplotlib

Both Linux and OSX are supported and binaries are provided on Pypi. We would like to support Windows but currently lack the expertise to do so. If you would like to take on the Windows release and maintenance, please open an issue and we'll try to help.

A source package which should not require Cython nor SWIG is also provided on Pypi.

To develop HTSeq you will also need:

• Cython >=0.29.5
• SWIG >=3.0.8

Installation

PIP

To install directly from PyPI:

pip install HTSeq

To install a specific version:

pip install 'HTSeq==0.14.0'

If this fails, please install all dependencies first:

pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq

setup.py (distutils/setuptools)

Install the dependencies with your favourite tool (pip, conda, etc.).

To install HTSeq itself, run:

python setup.py build install

Authors

• 2016-: Fabio Zanini @ http://fabilab.org.
• 2010-2015: Simon Anders, Wolfgang Huber