Package: BulkSignalR
Type: Package
Title: Infer Ligand-Receptor Interactions from bulk expression
        (transcriptomics/proteomics) data, or spatial transcriptomics
Version: 1.0.2
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, 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
Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>=
        3.0.0), codetools, Matrix, lattice, cluster, survival, MASS,
        nlme
Config/testthat/edition: 3
RoxygenNote: 7.3.2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_21
git_last_commit: 96995d4
git_last_commit_date: 2025-05-21
Repository: Bioconductor 3.21
Date/Publication: 2025-05-22
NeedsCompilation: no
Packaged: 2025-05-22 21:42:01 UTC; biocbuild
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 4.5.0; ; 2025-05-23 16:20:05 UTC; unix
