This is the development version of dominoSignal; for the stable release version, see dominoSignal.
Cell Communication Analysis for Single Cell RNA SequencingBioconductor version: Development (3.22)
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.
Author: Christopher Cherry [aut] ORCID: 0000-0002-5481-0055 , Jacob T Mitchell [aut, cre] ORCID: 0000-0002-5370-9692 , Sushma Nagaraj [aut] ORCID: 0000-0001-5166-1309 , Kavita Krishnan [aut] ORCID: 0000-0003-1345-0249 , Dmitrijs Lvovs [aut], Elana Fertig [ctb] ORCID: 0000-0003-3204-342X , Jennifer Elisseeff [ctb] ORCID: 0000-0002-5066-1996
Maintainer: Jacob T Mitchell <jmitch81 at jhmi.edu>
Citation (from within R, entercitation("dominoSignal")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("dominoSignal")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dominoSignal")Follow Installation instructions to use this package in your R session.
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