Package: scDiffCom
Type: Package
Title: Differential Analysis of Intercellular Communication from
        scRNA-Seq Data
Version: 1.2.0
Authors@R: c(
    person("Cyril", "Lagger", email = "lagger.cyril@gmail.com",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-1701-6896")
    ),
    person("Eugen", "Ursu", email = "ursu_eugen@hotmail.com",
    role = c("aut")),
    person("Anais", "Equey", email = "anais.equey@gmail.com",
    role = c("ctb"))
    )
Description: Analysis tools to investigate changes in intercellular
        communication from scRNA-seq data. Using a Seurat object as
        input, the package infers which cell-cell interactions are
        present in the dataset and how these interactions change
        between two conditions of interest (e.g. young vs old). It
        relies on an internal database of ligand-receptor interactions
        (available for human, mouse and rat) that have been gathered
        from several published studies. Detection and differential
        analyses rely on permutation tests. The package also contains
        several tools to perform over-representation analysis and
        visualize the results. See Lagger, C. et al. (2023)
        <doi:10.1038/s43587-023-00514-x> for a full description of the
        methodology.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
RoxygenNote: 7.3.3
biocViews:
Suggests: biomaRt, covr, DT, ggplot2, GOSemSim, igraph, kableExtra,
        KEGGREST, knitr, ontologyIndex, ontoProc, pkgdown, plotly,
        RColorBrewer, rmarkdown, rrvgo, spelling, shiny, shinythemes,
        shinyWidgets, testthat (>= 3.0.0), visNetwork
Imports: data.table, DelayedArray, future, future.apply, lifecycle,
        magrittr, methods, Seurat (>= 5.0.0), stats, utils
Collate: 'data.R' 'interaction_analysis.R' 'objects.R' 'utils_LRI.R'
        'utils_cci.R' 'utils_filtering.R' 'utils_interactiveNetworks.R'
        'utils_ora.R' 'utils_permutation.R' 'utils_preprocessing.R'
        'utils_validation.R' 'utils_shiny.R'
URL: https://cyrillagger.github.io/scDiffCom/,
        https://github.com/CyrilLagger/scDiffCom
Language: en-US
Config/testthat/edition: 3
BugReports: https://github.com/CyrilLagger/scDiffCom/issues
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://cyrillagger.r-universe.dev
Date/Publication: 2025-10-14 14:20:39 UTC
RemoteUrl: https://github.com/cyrillagger/scdiffcom
RemoteRef: HEAD
RemoteSha: febe137bcb460b23d2082d56a539639481925d44
NeedsCompilation: no
Packaged: 2026-10-09 08:58:46 UTC; root
Author: Cyril Lagger [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1701-6896>),
  Eugen Ursu [aut],
  Anais Equey [ctb]
Maintainer: Cyril Lagger <lagger.cyril@gmail.com>