dominoSignal

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

Cell Communication Analysis for Single Cell RNA Sequencing

Bioconductor version: Development (3.21)

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: ), Jacob T Mitchell [aut, cre] (ORCID: ), Sushma Nagaraj [aut] (ORCID: ), Kavita Krishnan [aut] (ORCID: ), Dmitrijs Lvovs [aut], Elana Fertig [ctb] (ORCID: ), Jennifer Elisseeff [ctb] (ORCID: )

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

Citation (from within R, enter citation("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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dominoSignal")

Get Started with dominoSignal	HTML	R Script
Interacting with domino Objects	HTML	R Script
Plotting Functions and Options	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Network, SingleCell, Software, SystemsBiology, Transcriptomics
Version	1.1.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
License	GPL-3 \| file LICENSE
Depends	R (>= 4.2.0)
Imports	biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils
System Requirements
URL	https://fertiglab.github.io/dominoSignal/
Bug Reports	https://github.com/FertigLab/dominoSignal/issues

Suggests	knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	dominoSignal_1.1.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/dominoSignal
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dominoSignal
Bioc Package Browser	https://code.bioconductor.org/browse/dominoSignal/
Package Short Url	https://bioconductor.org/packages/dominoSignal/
Package Downloads Report	Download Stats