recipe isoquant

IsoQuant is a tool for reference-based analysis of long RNA reads, such as gene/transcript quantification and discovery.






package isoquant

(downloads) docker_isoquant



depends argcomplete:


depends argh:


depends biopython:


depends gffutils:


depends minimap2:


depends pandas:


depends pybedtools:


depends pyfaidx:


depends pysam:


depends python:


depends samtools:


depends simplejson:


depends six:




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 isoquant

and update with::

   mamba update isoquant

To create a new environment, run:

mamba create --name myenvname isoquant

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 `isoquant/tags`_ for valid values for ``<tag>``)

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