dominoSignal

This is the development version of dominoSignal; to use it, please install the devel version of Bioconductor.

Cell Communication Analysis for Single Cell RNA Sequencing


Bioconductor version: Development (3.20)

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

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

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

Installation

To install this package, start R (version "4.4") 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
NEWS Text
LICENSE Text

Details

biocViews Network, SingleCell, Software, SystemsBiology, Transcriptomics
Version 0.99.4
In Bioconductor since BioC 3.20 (R-4.4)
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
See More
Suggests knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package dominoSignal_0.99.4.tar.gz
Windows Binary dominoSignal_0.99.4.zip
macOS Binary (x86_64) dominoSignal_0.99.4.tgz
macOS Binary (arm64) dominoSignal_0.99.4.tgz
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