recipe cascade-reg

Causal discovery of gene regulatory programs from single-cell genomics

Homepage:

https://github.com/gao-lab/CASCADE

Documentation:

https://cascade-reg.readthedocs.io

License:

MIT / MIT

Recipe:

/cascade-reg/meta.yaml

CASCADE stands for Causality-Aware Single-Cell Adaptive Discover/Deduction/Design Engine. It is a deep learning-based bioinformatics tool for causal gene regulatory network discovery, counterfactual perturbation effect prediction, and targeted intervention design based on high-content single-cell perturbation screens.

package cascade-reg

versions:

0.5.1-0

depends adjusttext:

depends anndata:

depends kneed:

depends loguru:

depends matplotlib-base:

depends networkx:

depends numpy:

depends pandas:

depends pynvml:

depends python:

depends pytorch:

>=2

depends pytorch-lightning:

>=2

depends pyyaml:

depends rich:

depends scanpy:

depends scikit-learn:

depends scipy:

depends seaborn:

depends tensorboard:

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 cascade-reg

and update with::

   mamba update cascade-reg

To create a new environment, run:

mamba create --name myenvname cascade-reg

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/cascade-reg:<tag>

(see `cascade-reg/tags`_ for valid values for ``<tag>``)

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