[](https://htseq.readthedocs.io)
# HTSeq
**DEVS**: https://github.com/htseq/htseq
**DOCS**: https://htseq.readthedocs.io
**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022).
A Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq``
is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq
and similar experiments.
## Requirements
To use ``HTSeq`` you need:
- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped)
- ``numpy``
- ``pysam``
To manipulate BigWig files, you also need:
- ``pyBigWig``
To run the ``htseq-qa`` script, you also need:
- ``matplotlib``
To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need:
- ``mtx`` file: ``scipy``
- ``h5ad`` file: ``anndata``
- ``loom`` file: ``loompy``
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==2.0.0'
```
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
```
## Testing
To test locally, run
```bash
./test.sh
```
To test `htseq-count` alone, run it with the `-o` option.
A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts.
## Authors
- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber