scMetaLink/DESCRIPTION at main · WaveoffBioMed/scMetaLink · GitHub

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Package: scMetaLink
Type: Package
Title: Single-Cell Metabolite-Mediated Cell Communication Analysis
Version: 0.99.1
Date: 2026-01-26
Authors@R: person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0002-0452-742X"))
Author: Zaoqu Liu [aut, cre] (<https://orcid.org/0000-0002-0452-742X>)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>
Description: A comprehensive framework for inferring metabolite-mediated cell-cell
    communication from single-cell transcriptomic data. scMetaLink integrates
    metabolite production potential via enzyme expression, metabolite sensing
    capability via receptor and transporter expression, and secretion potential
    to construct intercellular metabolic communication networks. The package
    leverages the MetalinksDB database containing 41894 metabolite-protein
    interactions covering 1128 metabolites and 4374 proteins. Key features
    include probabilistic inference of metabolite production, receptor-mediated
    metabolite sensing quantification, permutation-based statistical testing
    with multiple hypothesis correction, pathway-level aggregation analysis,
    and publication-ready visualization.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Depends:
    R (>= 4.0.0)
Imports:
    methods,
    stats,
    utils,
    grDevices,
    graphics,
    Matrix,
    ggplot2,
    ggraph,
    igraph,
    scales,
    circlize,
    ComplexHeatmap,
    grid,
    viridis,
    RColorBrewer,
    future,
    future.apply
Suggests:
    Seurat (>= 4.0.0),
    SingleCellExperiment,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    BiocStyle,
    reshape2,
    pkgdown
VignetteBuilder: knitr
biocViews:
    Software,
    SingleCell,
    Transcriptomics,
    CellBiology,
    Metabolomics,
    Network,
    Visualization,
    GeneExpression,
    Spatial
RoxygenNote: 7.3.3
Config/testthat/edition: 3
URL: https://github.com/Zaoqu-Liu/scMetaLink, https://Zaoqu-Liu.github.io/scMetaLink/
BugReports: https://github.com/Zaoqu-Liu/scMetaLink/issues