Skip to main content
Python Software Foundation 20th Year Anniversary Fundraiser  Donate today!

A framework to process and analyze data from high-throughput sequencing (HTS) assays

Project description

CI Documentation Status

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

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for HTSeq, version 0.13.5
Filename, size File type Python version Upload date Hashes
Filename, size HTSeq-0.13.5-cp36-cp36m-macosx_10_9_x86_64.whl (296.2 kB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp36-cp36m-manylinux2010_x86_64.whl (1.3 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp37-cp37m-macosx_10_9_x86_64.whl (289.3 kB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp37-cp37m-manylinux2010_x86_64.whl (1.3 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp38-cp38-macosx_10_9_x86_64.whl (294.3 kB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp38-cp38-manylinux2010_x86_64.whl (1.6 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp39-cp39-macosx_10_9_x86_64.whl (272.7 kB) File type Wheel Python version cp39 Upload date Hashes View
Filename, size HTSeq-0.13.5-cp39-cp39-manylinux2010_x86_64.whl (1.5 MB) File type Wheel Python version cp39 Upload date Hashes View
Filename, size HTSeq-0.13.5.tar.gz (318.1 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page