Package Recipe 'genecircuitry'

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
Links:: pypi: :pypi:`genecircuitry`

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:

0.1.7-0, 0.1.4-0

Depends:

on adjusttext >=0.7.3
on anndata >=0.8.0
on fa2_modified
on genomepy >=0.8.4
on gimmemotifs >=0.14.4
on goatools
on gseapy
on h5py >=3.1.0
on igraph >=0.10.1
on joblib
on jupyter
on leidenalg
on louvain
on matplotlib-base >=3.6.3
on networkx >=2.6.0
on numba >=0.50.1
on numpy >=1.20
on pandas >=1.3.0
on pyarrow >=0.17
on python >=3.9,<3.11
on scanpy >=1.9.0
on scikit-learn
on scipy
on seaborn
on tqdm >=4.45
on umap-learn
on velocyto.py >=0.17
on weasyprint

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 genecircuitry

to add into an existing workspace instead, run:

pixi add genecircuitry

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 genecircuitry

Alternatively, to install into a new environment, run:

conda create -n envname genecircuitry

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/genecircuitry:<tag>

(see genecircuitry/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/genecircuitry/README.html)