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 (3.24)
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 activity (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] , Sushma Nagaraj [aut] , Kavita Krishnan [aut, cre] , Dmitrijs Lvovs [aut], Elana Fertig [ctb] , Jennifer Elisseeff [ctb]
Maintainer: Kavita Krishnan <kkrishnan at som.umaryland.edu>
citation("dominoSignal")):Christopher Cherry, Jacob T Mitchell, Sushma Nagaraj, Kavita Krishnan, Dmitrijs Lvovs. dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing. doi:10.18129/B9.bioc.dominoSignal, R package version 1.7.1, https://bioconductor.org/packages/dominoSignal.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Differential Signaling Workflow | HTML | R Script |
| Interacting with domino Objects | HTML | R Script |
| Get Started with dominoSignal | HTML | R Script |
| Plotting Functions and Options | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Network, Sequencing, SingleCell, Software, SystemsBiology, Transcriptomics |
| Version | 1.7.1 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 4.2.0) |
| Imports | biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, reshape2, stats, utils, purrr, dplyr |
| 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, withr, kableExtra |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dominoSignal_1.7.1.tar.gz |
| Windows Binary (x86_64) | dominoSignal_1.7.1.zip |
| macOS Binary (big-sur-x86_64) | dominoSignal_1.7.1.tgz |
| macOS Binary (sonoma-arm64) | dominoSignal_1.7.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dominoSignal |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dominoSignal |
| Package Short Url | https://bioconductor.org/packages/dominoSignal/ |
| Package Downloads Report | Download Stats |