dominoSignal
This is the released version of dominoSignal; for the devel version, see dominoSignal.
Cell Communication Analysis for Single Cell RNA Sequencing
Bioconductor version: Release (3.23)
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]
, 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.6.0 |
| 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, stats, utils, magrittr, 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 |
| 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | dominoSignal_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | dominoSignal_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | dominoSignal_1.6.0.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 |