[](https://htseq.readthedocs.io)
# 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:
```bash
pip install HTSeq
```
To install a specific version:
```bash
pip install 'HTSeq==0.14.0'
```
If this fails, please install all dependencies first:
```bash
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:
```bash
python setup.py build install
```
## Authors
- Since 2016: Fabio Zanini @ http://fabilab.org.
- 2020-2015: Simon Anders, Wolfgang Huber