A framework to process and analyze data from high-throughput sequencing (HTS) assays
Project description
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 2.7
orPython >= 3.5
numpy
pysam >= 0.9.0
To run the htseq-qa
script, you will also need:
matplotlib >=1.4
Both Linux and OSX are supported and binaries are provided on Pypi.
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
Windows is not officially supported as we don't have access to a Continuous
Integration Windows machine that supports pysam
. Please do not open an
issue asking to support Windows installers: we do not know how to do that and
do not have the bandwidth to learn. However, if you are interested in giving it
a try yourself, we are happy to provide as much support as we can.
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>=1.4'
pip install Cython
pip install 'pysam>=0.9'
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
- Since 2016: Fabio Zanini @ http://fabilab.org.
- 2020-2015: Simon Anders, Wolfgang Huber
Project details
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