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Bioconductor - BulkSignalR

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

Bioconductor version: Release (3.21)

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")): 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")
Details biocViews Network, NetworkInference, Proteomics, RNASeq, Software, Spatial, Transcriptomics Version 1.0.2 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License CeCILL | file LICENSE Depends R (>= 4.5) Imports BiocFileCache, httr, DBI, RCurl, RSQLite, cli, curl, dplyr, 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 See More Suggests knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme 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.

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