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.
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
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
Install the dependencies with your favourite tool (pip
, conda
,
etc.).
To install HTSeq
itself, run:
python setup.py build install
- 2016-: Fabio Zanini @ http://fabilab.org.
- 2010-2015: Simon Anders, Wolfgang Huber