- recipe snp2cell
A package for finding enriched regulatory networks from GWAS and single cell data.
- Homepage:
- License:
BSD / BSD-3-Clause
- Recipe:
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:
0.3.0-0,0.2.2-0,0.2.1-0,0.2.0-0- Depends:
on dill
on joblib
on matplotlib-base
on networkx
on numpy
on pandas
on pybiomart
on pyranges
on python
>=3.8,<3.12on rich
on scanpy
on scipy
on seaborn
on statsmodels
on tqdm
on typer
on typing_extensions
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install snp2cell
to add into an existing workspace instead, run:
pixi add snp2cell
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install snp2cell
Alternatively, to install into a new environment, run:
conda create -n envname snp2cell
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/snp2cell:<tag>
(see snp2cell/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/snp2cell/README.html)
