SingleCellSignalR

This is the released version of SingleCellSignalR; for the devel version, see SingleCellSignalR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Cell Signalling Using Single-Cell RNA-seq or Proteomics Data

Bioconductor version: Release (3.23)

Inference of ligand-receptor (L-R) interactions from single-cell expression (transcriptomics/proteomics) data. SingleCellSignalR v2 inferences rely on the statistical model we introduced in the BulkSignalR package as well as the original SingleCellSignalR LR-score (both are available). SingleCellSignalR v2 can be regarded as a wrapper to BulkSignalR fundamental classes. This also enables v2 users to work with any species, whereas only Mus musculus & Homo sapiens were available before in SingleCellSignalR v1.

Author: Jacques Colinge [aut] ORCID: 0000-0003-2466-4824 , Jean-Philippe Villemin [cre] ORCID: 0000-0002-1838-5880

Maintainer: Jean-Philippe Villemin <jpvillemin at gmail.com>

Citation (from within R, enter citation("SingleCellSignalR")):

Jacques Colinge. SingleCellSignalR: Cell Signalling Using Single-Cell RNA-seq or Proteomics Data. doi:10.18129/B9.bioc.SingleCellSignalR, R package version 2.2.0, https://bioconductor.org/packages/SingleCellSignalR.

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")

BiocManager::install("SingleCellSignalR")

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("SingleCellSignalR")

SingleCellSignalR-Main	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Network, NetworkInference, Proteomics, RNASeq, SingleCell, Software, Transcriptomics
Version	2.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	CeCILL \| file LICENSE
Depends	R (>= 4.5)
Imports	stats, utils, methods, ggplot2, matrixTests, matrixStats, foreach, BulkSignalR, grid, ComplexHeatmap, circlize
System Requirements
URL	https://github.com/jcolinge/SingleCellSignalR
Bug Reports	https://github.com/jcolinge/SingleCellSignalR/issues

Suggests	knitr, markdown, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	tidySingleCellExperiment
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SingleCellSignalR_2.2.0.tar.gz
Windows Binary (x86_64)	SingleCellSignalR_2.2.0.zip
macOS Binary (big-sur-x86_64)	SingleCellSignalR_2.2.0.tgz
macOS Binary (sonoma-arm64)	SingleCellSignalR_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SingleCellSignalR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SingleCellSignalR
Package Short Url	https://bioconductor.org/packages/SingleCellSignalR/
Package Downloads Report	Download Stats