recipe genecircuitry

GeneCircuitry: TRN analysis from single-cell data (Scanpy, CellOracle, Hotspot)

Homepage:

https://github.com/samuelecancellieri/genecircuitry

Documentation:

https://github.com/samuelecancellieri/genecircuitry/blob/main/README.md

License:

MIT / MIT

Recipe:

/genecircuitry/meta.yaml

A modular, checkpoint-enabled pipeline for TRN analysis from single-cell RNA-seq data. Integrates Scanpy for preprocessing and clustering, CellOracle for GRN inference, and Hotspot for embedding-aware gene modules identification. Provides an HTML/PDF reporting layer and a standalone ``genecircuitry`` CLI entry point.

package genecircuitry

versions:

0.1.4-0

depends adjusttext:

>=0.7.3

depends anndata:

>=0.8.0

depends fa2_modified:

depends genomepy:

>=0.8.4

depends gimmemotifs:

>=0.14.4

depends goatools:

depends gseapy:

depends h5py:

>=3.1.0

depends igraph:

>=0.10.1

depends joblib:

depends jupyter:

depends leidenalg:

depends louvain:

depends matplotlib-base:

>=3.6.3

depends networkx:

>=2.6.0

depends numba:

>=0.50.1

depends numpy:

>=1.20

depends pandas:

>=1.3.0

depends pyarrow:

>=0.17

depends python:

>=3.9,<3.11

depends scanpy:

>=1.9.0

depends scikit-learn:

depends scipy:

depends seaborn:

depends tqdm:

>=4.45

depends umap-learn:

depends velocyto.py:

>=0.17

depends weasyprint:

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 genecircuitry

and update with::

   mamba update genecircuitry

To create a new environment, run:

mamba create --name myenvname genecircuitry

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/genecircuitry:<tag>

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

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