BulkSignalR

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

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

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DOI: 10.18129/B9.bioc.BulkSignalR

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0003-2466-4824 , Jean-Philippe Villemin [cre] ORCID iD ORCID: 0000-0002-1838-5880

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

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

Installation

To install this package, start R (version "4.5") 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 1.2.1

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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/ZheFrench/BulkSignalR

Bug Reports https://github.com/ZheFrench/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

Package Archives

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

Source Package BulkSignalR_1.2.1.tar.gz

Windows Binary (x86_64) BulkSignalR_1.1.4.zip

macOS Binary (x86_64) BulkSignalR_1.2.0.tgz

macOS Binary (arm64) BulkSignalR_1.2.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/BulkSignalR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BulkSignalR

Bioc Package Browser https://code.bioconductor.org/browse/BulkSignalR/

Package Short Url https://bioconductor.org/packages/BulkSignalR/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.22 Source Archive