Package: HuMMuS

Title: Heterogeneous Multilayer Network for Multi-Omics Single-Cell Data

Version: 0.0.2

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/