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Bioconductor - dominoSignal (development version)

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 (3.22)

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, 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")
Details biocViews Network, SingleCell, Software, SystemsBiology, Transcriptomics Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License GPL-3 | file LICENSE Depends R (>= 4.2.0) Imports biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr System Requirements URL https://fertiglab.github.io/dominoSignal/ Bug Reports https://github.com/FertigLab/dominoSignal/issues See More Package Archives

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

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