Package: BulkSignalR
Type: Package
Title: Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Version: 1.3.1
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 (>= 4.5)
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
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: e236c5a
git_last_commit_date: 2025-11-08
Repository: Bioconductor 3.23
