HTSeq

DEVS: https://github.com/htseq/htseq

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 2 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:

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

Metadata

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)

Source distribution for HTSeq 2.1.2
File	Size	Uploaded	Provenance
htseq-2.1.2.tar.gz	506.2 kB	Feb 4, 2026	Without provenance	Details

Built distributions (wheels)

Table of built distributions (wheels) for HTSeq 2.1.2
File	Interpreter	ABI	Platform	Reset
htseq-2.1.2-cp313-cp313t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 2.1 MB Feb 4, 2026 Without provenance	CPython 3.13	CPython 3.13 free-threading	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
htseq-2.1.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 2.1 MB Feb 4, 2026 Without provenance	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
htseq-2.1.2-cp313-cp313-macosx_10_15_x86_64.whl 333.2 kB Feb 4, 2026 Without provenance	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 2.1 MB Feb 4, 2026 Without provenance	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
htseq-2.1.2-cp312-cp312-macosx_10_15_x86_64.whl 333.7 kB Feb 4, 2026 Without provenance	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 2.1 MB Feb 4, 2026 Without provenance	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 331.7 kB Feb 4, 2026 Without provenance	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 2.0 MB Feb 4, 2026 Without provenance	CPython 3.10	CPython 3.10	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
htseq-2.1.2-cp310-cp310-macosx_10_15_x86_64.whl 332.6 kB Feb 4, 2026 Without provenance	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
SHA-256 checksum How to use checksums	`69d5a6b9a832ea85edf8a32fbac591a8af2e32bb961d1f3843c48c9d03a77a82`
BLAKE2b-256 checksum How to use checksums	`034c6ad404122b3a872f76c5d6e2a73dd992861a582d0c7b7269453bf8943ce2`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.12.12`

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
SHA-256 checksum How to use checksums	`0b2aaa800c64c4726afa522abc74ba64b789ba15d3e01c84b66ffc3300bc01a5`
BLAKE2b-256 checksum How to use checksums	`5a4ff4b339c8719bb20820af73237529caec5d75da2deb3c8fa7f9977b310c34`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.11`

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
Tags	CPython 3.13 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`a9a79febc9744c2490cdc4fbe71f52ef9a1dc7c8cedd4fd344b6b4dccfa0eef9`
BLAKE2b-256 checksum How to use checksums	`250e87f0df958babfed8e6e446aec787bcc9c3a54a5bffcbe230247e1bd7e131`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.11`

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
Tags	CPython 3.13 macOS 10.15+ x86-64
SHA-256 checksum How to use checksums	`d6a36c85160628bcfa03b60dad74646d96f3d776371d79a8b29bcb09d958ac69`
BLAKE2b-256 checksum How to use checksums	`1d4342cf9d2f2748cea161277e95fc5cbd42c91151a226caf643651174292d86`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.5`

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
SHA-256 checksum How to use checksums	`b425a1f1c84695e04da4c8ec7ea4addd08cf3412cbb883893150bd78eac8b3c0`
BLAKE2b-256 checksum How to use checksums	`1f13cff80ba4e3b7e8070cba7393261662dd863e4f20c45807469d646495aed8`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.12.12`

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
Size	333.7 kB
Tags	CPython 3.12 macOS 10.15+ x86-64
SHA-256 checksum How to use checksums	`480a2f9a16e9d76d7a69b99f7ae9b0fe77b549e7ef2b747654853c716c3a6fe2`
BLAKE2b-256 checksum How to use checksums	`33c907fda72fce1611fbd282e95bb038e328c1182964466cad455a9519e7f3c5`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.12.11`

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
SHA-256 checksum How to use checksums	`3645134cab3440d6cdea7c36ede1add1f7663a415fbf4a95a639bf1d5a475ebe`
BLAKE2b-256 checksum How to use checksums	`5ce98a8e9af09b346265ffd367fef1d056f77649121e7496765e69fe7e229e6e`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.11.14`

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
Size	331.7 kB
Tags	CPython 3.11 macOS 10.15+ x86-64
SHA-256 checksum How to use checksums	`6d4b66b633f0a7e6d88a2b823a2201e0b582cdcf2140c3d2bf6df7a9d4f8250d`
BLAKE2b-256 checksum How to use checksums	`7cee398068744f12fdc23e81293a9d5368b67f9fc928660d7f42073a93fcb252`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.11.13`

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
Size	2.0 MB
Tags	CPython 3.10 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`a1b3940b3c4a9b12a6e9b2ebe93d5f3a83fa9a0305a4652594ce8d308b3d8544`
BLAKE2b-256 checksum How to use checksums	`8403c8c786f6502d9e2b500c8cadb7bcea9467e7148bf5d58165427b92e10fc4`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.10.19`

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
Size	332.6 kB
Tags	CPython 3.10 macOS 10.15+ x86-64
SHA-256 checksum How to use checksums	`1845a1b17adf5aac1831545bfc3dfbaecb0ffc29238b7344fd19474a70e2fbdd`
BLAKE2b-256 checksum How to use checksums	`21ba291cbb7202fa49fbeec6577c043625c7c67869d823bd7d0e05320272cad0`
Upload date	Feb 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.10.18`

Security for HTSeq 2.1.2

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