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 (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 >= 3.10(note:Python 2support has been dropped)numpypysam
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:
mtxfile:scipyh5adfile:anndataloomfile: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 >=0.29.5SWIG >=3.0.8
Installation
PIP
To install directly from PyPI:
pip install HTSeq
To install a specific version:
pip install 'HTSeq==2.0.0'
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
Testing
To test locally, run
./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)
- 2016-: Fabio Zanini (iosonofabio)@ https://fabilab.org
- 2010-2015: Simon Anders (simon-anders), Wolfgang Huber
3 maintainers
Release files for HTSeq 2.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| htseq-2.1.2.tar.gz | 506.2 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| htseq-2.1.2-cp313-cp313t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 free-threading | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| htseq-2.1.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| htseq-2.1.2-cp313-cp313-macosx_10_15_x86_64.whl | CPython 3.13 | CPython 3.13 | macOS 10.15+ x86-64 | Details |
| htseq-2.1.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| htseq-2.1.2-cp312-cp312-macosx_10_15_x86_64.whl | CPython 3.12 | CPython 3.12 | macOS 10.15+ x86-64 | Details |
| htseq-2.1.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| htseq-2.1.2-cp311-cp311-macosx_10_15_x86_64.whl | CPython 3.11 | CPython 3.11 | macOS 10.15+ x86-64 | Details |
| htseq-2.1.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 | Details |
| htseq-2.1.2-cp310-cp310-macosx_10_15_x86_64.whl | CPython 3.10 | CPython 3.10 | macOS 10.15+ x86-64 | Details |
Total release size: 12.3 MB
Release files / htseq-2.1.2.tar.gz
| Download URL | htseq-2.1.2.tar.gz |
|---|---|
| Size | 506.2 kB |
| Tags | Source |
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Release files / htseq-2.1.2-cp313-cp313t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | htseq-2.1.2-cp313-cp313t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 2.1 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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Release files / htseq-2.1.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | htseq-2.1.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 2.1 MB |
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Release files / htseq-2.1.2-cp313-cp313-macosx_10_15_x86_64.whl
| Download URL | htseq-2.1.2-cp313-cp313-macosx_10_15_x86_64.whl |
|---|---|
| Size | 333.2 kB |
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Release files / htseq-2.1.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | htseq-2.1.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 2.1 MB |
| Tags | CPython 3.12 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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Release files / htseq-2.1.2-cp312-cp312-macosx_10_15_x86_64.whl
| Download URL | htseq-2.1.2-cp312-cp312-macosx_10_15_x86_64.whl |
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| Size | 333.7 kB |
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Release files / htseq-2.1.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | htseq-2.1.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 2.1 MB |
| Tags | CPython 3.11 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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Release files / htseq-2.1.2-cp311-cp311-macosx_10_15_x86_64.whl
| Download URL | htseq-2.1.2-cp311-cp311-macosx_10_15_x86_64.whl |
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| Tags | CPython 3.11 macOS 10.15+ x86-64 |
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Release files / htseq-2.1.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | htseq-2.1.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
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| Tags | CPython 3.10 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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Release files / htseq-2.1.2-cp310-cp310-macosx_10_15_x86_64.whl
| Download URL | htseq-2.1.2-cp310-cp310-macosx_10_15_x86_64.whl |
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| Size | 332.6 kB |
| Tags | CPython 3.10 macOS 10.15+ x86-64 |
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