Package: BulkSignalR
Type: Package
Title: Infer Ligand-Receptor Interactions from bulk expression
        (transcriptomics/proteomics) data, or spatial transcriptomics
Version: 1.2.1
Authors@R: c(
    person("Jacques","Colinge",email="jacques.colinge@inserm.fr",role="aut",comment = c(ORCID = "0000-0003-2466-4824")),
    person("Jean-Philippe","Villemin",email="jpvillemin@gmail.com",role="cre",comment = c(ORCID = "0000-0002-1838-5880")))
Description: 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.
URL: https://github.com/ZheFrench/BulkSignalR
BugReports: https://github.com/ZheFrench/BulkSignalR/issues
License: CeCILL | file LICENSE
Encoding: UTF-8
LazyData: FALSE
Depends: R (>= 4.4)
biocViews: Network, RNASeq, Software, Proteomics, Transcriptomics,
        NetworkInference, Spatial
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
Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>=
        3.0.0), codetools, Matrix, lattice, cluster, survival, MASS,
        nlme
Config/testthat/edition: 3
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libmagick++-dev gsfonts
        libicu-dev libpng-dev libxml2-dev libssl-dev perl libx11-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-08 22:25:11 UTC
RemoteUrl: https://github.com/bioc/BulkSignalR
RemoteRef: RELEASE_3_22
RemoteSha: 68e85a5ed9af7d795192576c2b9da0db4401f2b0
NeedsCompilation: no
Packaged: 2026-01-24 23:16:58 UTC; root
Author: Jacques Colinge [aut] (ORCID: <https://orcid.org/0000-0003-2466-4824>),
  Jean-Philippe Villemin [cre] (ORCID:
    <https://orcid.org/0000-0002-1838-5880>)
Maintainer: Jean-Philippe Villemin <jpvillemin@gmail.com>
Built: R 4.5.2; ; 2026-01-24 23:19:37 UTC; windows
