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

Project description

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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 or Python >= 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

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Files for HTSeq, version 0.12.4
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Filename, size HTSeq-0.12.4-cp27-cp27m-macosx_10_7_x86_64.whl (312.1 kB) File type Wheel Python version cp27 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp27-cp27m-manylinux2010_x86_64.whl (1.2 MB) File type Wheel Python version cp27 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp27-cp27mu-manylinux2010_x86_64.whl (1.2 MB) File type Wheel Python version cp27 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp35-cp35m-manylinux2010_x86_64.whl (1.3 MB) File type Wheel Python version cp35 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp36-cp36m-macosx_10_9_x86_64.whl (326.9 kB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp36-cp36m-manylinux2010_x86_64.whl (1.4 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp37-cp37m-macosx_10_9_x86_64.whl (316.8 kB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp37-cp37m-manylinux2010_x86_64.whl (1.4 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp38-cp38-macosx_10_9_x86_64.whl (323.5 kB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size HTSeq-0.12.4-cp38-cp38-manylinux2010_x86_64.whl (1.6 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size HTSeq-0.12.4.tar.gz (625.8 kB) File type Source Python version None Upload date Hashes View

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