dominoSignal

This is the development version of dominoSignal; for the stable release version, see dominoSignal.

Cell Communication Analysis for Single Cell RNA Sequencing

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.dominoSignal

Bioconductor version: Development (3.23)

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 iD ORCID: 0000-0002-5481-0055 , Jacob T Mitchell [aut, cre] ORCID iD ORCID: 0000-0002-5370-9692 , Sushma Nagaraj [aut] ORCID iD ORCID: 0000-0001-5166-1309 , Kavita Krishnan [aut] ORCID iD ORCID: 0000-0003-1345-0249 , Dmitrijs Lvovs [aut], Elana Fertig [ctb] ORCID iD ORCID: 0000-0003-3204-342X , Jennifer Elisseeff [ctb] ORCID iD ORCID: 0000-0002-5066-1996

Maintainer: Jacob T Mitchell <jmitch81 at jhmi.edu>

Citation (from within R, enter citation("dominoSignal")):

Installation

To install this package, start R (version "4.6") 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.