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dominoSignal
This is thereleased version of dominoSignal; for the devel version, seedominoSignal.
Cell Communication Analysis for Single Cell RNA Sequencing
Bioconductor version: Release (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("dominoSignal")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("dominoSignal")For older versions of R, please refer to the appropriateBioconductor 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 | 1.4.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| License | GPL-3 | fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | dominoSignal_1.4.0.tar.gz |
| Windows Binary (x86_64) | dominoSignal_1.4.0.zip |
| macOS Binary (x86_64) | dominoSignal_1.4.0.tgz |
| macOS Binary (arm64) | dominoSignal_1.4.0.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 |