- recipe kompot
Differential abundance and gene expression analysis using Mahalanobis distance with JAX backend
- Homepage:
- Documentation:
- License:
GPL / GPL-3.0-or-later
- Recipe:
Kompot performs differential abundance and differential gene expression analysis using Gaussian process-based methods with Mahalanobis distance. It features a fast JAX backend and supports both Python API and CLI.
- package kompot¶
- versions:
0.6.0-0- depends anndata:
>=0.8.0- depends filelock:
>=3.12.0- depends jax:
>=0.3.0- depends jaxlib:
>=0.3.0- depends matplotlib-base:
>=3.5.0- depends mellon:
>=1.6.0- depends numpy:
>=1.20.0- depends pandas:
>=1.3.0- depends psutil:
>=5.9.0- depends pynndescent:
>=0.5.0- depends python:
>=3.9- depends python-igraph:
>=0.10.0- depends pyyaml:
>=5.0.0- depends scikit-learn:
>=1.0.0- depends scipy:
>=1.7.0- depends statsmodels:
>=0.13.0- depends tqdm:
>=4.60.0- 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 kompot and update with:: mamba update kompot
To create a new environment, run:
mamba create --name myenvname kompot
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/kompot:<tag> (see `kompot/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/kompot/README.html)
