BulkSignalR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

Bioconductor version: Release (3.23)

Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.

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("BulkSignalR")):

Jacques Colinge. BulkSignalR: Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. doi:10.18129/B9.bioc.BulkSignalR, R package version 1.4.0, https://bioconductor.org/packages/BulkSignalR.

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("BulkSignalR")

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("BulkSignalR")

BulkSignalR-Configure	HTML	R Script
BulkSignalR-Differential	HTML	R Script
BulkSignalR-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, Software, Spatial, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	CeCILL \| file LICENSE
Depends	R (>= 4.5)
Imports	BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite, matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2, gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph, orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>= 2.0.0), stats, scales, RANN, SpatialExperiment, SummarizedExperiment, tools
System Requirements
URL	https://github.com/jcolinge/BulkSignalR
Bug Reports	https://github.com/jcolinge/BulkSignalR/issues

Suggests	knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme
Linking To
Enhances
Depends On Me
Imports Me	SingleCellSignalR
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	BulkSignalR_1.4.0.tar.gz
Windows Binary (x86_64)	BulkSignalR_1.4.0.zip
macOS Binary (big-sur-x86_64)	BulkSignalR_1.4.0.tgz
macOS Binary (sonoma-arm64)	BulkSignalR_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BulkSignalR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BulkSignalR
Package Short Url	https://bioconductor.org/packages/BulkSignalR/
Package Downloads Report	Download Stats