DESCRIPTION

Package: HuMMuS
Title: Heterogeneous Multilayer Network for Multi-Omics Single-Cell Data
Version: 0.0.1
Authors@R: person(given = "Rémi",
    family = "Trimbour",
    email = "remi.trimbour@pasteur.fr",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0001-8770-8412"))
Description: A general framework to infer regulatory mechanisms from multi-omics single-cell data.
    HuMMuS package provides functions to build individual networks
    from different single-cell modalities, then to integrate them
    into a single-cell heterogeneous multilayer network. The package
    also provides functions to infer regulatory mechanisms from the
    heterogeneous multilayer network.
    HuMMuS is based on a flexible framework that can be adapted to any
    single-cell modalities. We provide study cases for scRNA+scATAC
    and scRNA+scATAC+snmC(methylation) that can be completed by PPI.
    Many regulatory mechanisms can be inferred with HuMMuS, notably
    classical gene regulatory networks (GRN), but TF-target genes,
    enhancer-gene interactions, TF-enhancer bindings, or even research
    of heterogeneous communnities of omics features (e.g. ensemble of
    peaks, genes and TFs cooperating to the same biological function).
License: AGPL (>= 3)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
    R (>= 4.0.0)
biocViews:
Imports:
    grr,
    sparseMatrixStats,
    TFBSTools,
    stringr,
    JASPAR2020,
    chromVAR,
    IRanges,
    Matrix,
    S4Vectors,
    utils,
    tidyr,
    OmnipathR,
    GENIE3,
    reshape2,
    Signac,
    biovizBase,
    SingleCellExperiment,
    motifmatchr,
    reticulate
Suggests:
    doParallel,
    doRNG,
    EnsDb.Hsapiens.v86,
    BSgenome.Hsapiens.UCSC.hg38,
    knitr,
    rmarkdown
VignetteBuilder: knitr
URL: https://cantinilab.github.io/HuMMuS/