dominoSignal
Cell Communication Analysis for Single Cell RNA Sequencing
Bioconductor version: Release (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("dominoSignal")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Network, SingleCell, Software, SystemsBiology, Transcriptomics |
| Version | 1.0.0 |
| 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 |
See More
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | dominoSignal_1.0.0.zip (64-bit only) |
| macOS Binary (x86_64) | dominoSignal_1.0.0.tgz |
| macOS Binary (arm64) | dominoSignal_1.0.0.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 |