- recipe gsmap
gsMap (genetically informed spatial mapping of cells for complex traits).
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
gsMap integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
- package gsmap¶
- Versions:
1.73.7-0,1.73.6-0,1.73.5-0,1.73.4-0,1.73.3-0,1.73.2-0,1.73.1-0,1.73.0-0,1.71.2-0,1.73.7-0,1.73.6-0,1.73.5-0,1.73.4-0,1.73.3-0,1.73.2-0,1.73.1-0,1.73.0-0,1.71.2-0,1.71.1-0,1.70-0- Depends:
on bitarray
on jinja2
on matplotlib-base
on numpy
<2.0.0on pandas
on plotly
on progress
on psutil
on pyarrow
on pyfiglet
on pyranges
on python
>=3.10on python-kaleido
on pyyaml
on scanpy
>=1.8on scikit-learn
on scikit-misc
on scipy
on seaborn-base
on tqdm
on zarr
- 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 gsmap
to add into an existing workspace instead, run:
pixi add gsmap
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 gsmap
Alternatively, to install into a new environment, run:
conda create -n envname gsmap
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/gsmap:<tag>
(see gsmap/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/gsmap/README.html)
