recipe htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.



GPL / GPL-3.0-only




biotools: htseq, usegalaxy-eu: htseq_count, doi: 10.1093/bioinformatics/btu638

package htseq

(downloads) docker_htseq



depends libgcc-ng:


depends libstdcxx-ng:


depends matplotlib-base:


depends numpy:


depends pandas:


depends pysam:


depends pysam:


depends python:


depends python_abi:

3.10.* *_cp310

depends scipy:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install htseq

and update with::

   mamba update htseq

To create a new environment, run:

mamba create --name myenvname htseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `htseq/tags`_ for valid values for ``<tag>``)

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