recipe snp2cell

A package for finding enriched regulatory networks from GWAS and single cell data.

Homepage:

https://github.com/Teichlab/snp2cell

License:

BSD / BSD-3-Clause

Recipe:

/snp2cell/meta.yaml

A package for identifying gene regulation involved in specific traits and cell types. It combines three elements: (i) GWAS summary statistics, (ii) single cell data and (iii) a base gene regulatory network.

package snp2cell

versions:

0.2.0-0

depends dill:

depends joblib:

depends matplotlib-base:

depends networkx:

depends numpy:

depends pandas:

depends pybiomart:

depends pyranges:

depends python:

>=3.8,<3.12

depends rich:

depends scanpy:

depends scipy:

depends seaborn:

depends statsmodels:

depends tqdm:

depends typer:

depends typing_extensions:

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 snp2cell

and update with::

   mamba update snp2cell

To create a new environment, run:

mamba create --name myenvname snp2cell

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/snp2cell:<tag>

(see `snp2cell/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an badge with the following MarkDown:

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