recipe pytximport

pytximport - gene count estimation from transcript-level quantification

Homepage:

https://pytximport.readthedocs.io/en/stable/start.html

Documentation:

https://pytximport.readthedocs.io

Developer docs:

https://github.com/complextissue/pytximport

License:

GPL / GPL-3.0-only

Recipe:

/pytximport/meta.yaml

pytximport is a Python port of tximport that allows users to import transcript counts from tools such as kallisto and Salmon, correct them for differential isoform usage, and summarize them at the gene level.

package pytximport

(downloads) docker_pytximport

versions:

0.11.0-0,  0.10.0-0,  0.9.0-0,  0.8.0-0,  0.7.0-0,  0.6.0-0

depends anndata:

>=0.8.0

depends click:

>=8.1.7

depends click-default-group:

>=1.2.0

depends flox:

>=0.9.8

depends h5py:

>=3.11.0

depends numpy:

>=1.23.0

depends pandas:

>=1.4.0

depends pybiomart:

>=0.2.0

depends python:

>=3.9

depends tqdm:

>=4.66.4

depends xarray:

>=2024.6.0

requirements:

additional platforms:

Installation

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 pytximport

and update with::

   mamba update pytximport

To create a new environment, run:

mamba create --name myenvname pytximport

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 quay.io/biocontainers/pytximport:<tag>

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

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Link to this page

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