- recipe pytximport
pytximport - gene count estimation from alignment-free quantification
- Homepage:
- Documentation:
- Developer docs:
- License:
GPL / GPL-3.0-only
- Recipe:
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¶
- versions:
0.8.0-0,0.7.0-0,0.6.0-0- depends anndata:
>=0.8.0- depends click:
>=8.1.7- depends dask:
>=2024.7.0- 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:
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
myenvnamebeing 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>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pytximport/README.html)
