recipe bioconductor-dominosignal

Cell Communication Analysis for Single Cell RNA Sequencing

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/dominoSignal.html

License:

GPL-3 | file LICENSE

Recipe:

/bioconductor-dominosignal/meta.yaml

dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.

package bioconductor-dominosignal

(downloads) docker_bioconductor-dominosignal

versions:

1.0.0-0

depends bioconductor-biomart:

>=2.62.0,<2.63.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends r-base:

>=4.4,<4.5.0a0

depends r-circlize:

depends r-ggpubr:

depends r-igraph:

depends r-matrix:

depends r-plyr:

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 bioconductor-dominosignal

and update with::

   mamba update bioconductor-dominosignal

To create a new environment, run:

mamba create --name myenvname bioconductor-dominosignal

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/bioconductor-dominosignal:<tag>

(see `bioconductor-dominosignal/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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/bioconductor-dominosignal/README.html)