SigBridgeR/DESCRIPTION at main · WangLabCSU/SigBridgeR · GitHub

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Package: SigBridgeR
Title: Integrative Toolkit for Linking Phenotypes to Cell Subpopulations via scRNA-seq and Bulk Data
Version: 3.8.1
Authors@R:
    c(
        person("Yuxi", "Yang", email = "15364051195@163.com", role = c("cre", "aut"), comment = c(ORCID = "0009-0006-1329-1224")),
        person("Shixiang", "Wang", email = "shixiang1994wang@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0001-9855-7357")),
        person("Zeyu", "Yan", email = "3191647388@qq.com", role = "ctb")
     )
Description: Identifies phenotype-associated cell subpopulations by integrating phenotypic data (e.g., survival, drug sensitivity), bulk gene expression, and single-cell RNA-seq (scRNA-seq) profiles. It employs multiple algorithms to reliably connect cellular features with clinical or functional phenotypes, offering a unified pipeline for multi-modal analysis that uncovers biologically and clinically relevant cell states in heterogeneous datasets.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://wanglabcsu.github.io/sigbridger
BugReports: https://github.com/WangLabCSU/SigBridgeR/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports:
    chk,
    cli,
    data.table,
    dplyr,
    IDConverter,
    Matrix,
    purrr,
    rlang (>= 1.0.0),
    scAB (>= 1.0.4),
    Scissor (>= 2.0.1),
    Seurat (>= 5.0.0),
    SeuratObject (>= 5.0.0),
    SigBridgeRUtils (>= 0.2.5)
Depends:
    R (>= 4.1.0)
Remotes:
    github::Exceret/ALRA,
    github::Exceret/DEGAS,
    github::Exceret/LPSGL,
    github::Exceret/PIPET,
    github::Exceret/rTiRank,
    github::Exceret/rSIDISH,
    github::Exceret/scAB,
    github::Exceret/SCIPAC,
    github::Exceret/Scissor,
    github::Exceret/scPAS,
    github::Exceret/ScPP,
    github::ShixiangWang/IDConverter,
    github::yonicd/tidycheckUsage
Suggests:
    ALRA,
    anndata,
    anndataR,
    BiocManager,
    carrier,
    celldex,
    cheapr,
    codetools,
    curl,
    DEGAS,
    edgeR,
    furrr,
    future,
    future.mirai,
    ggforce,
    ggplot2,
    ggupset,
    ggVennDiagram,
    glue,
    here,
    jsonlite,
    KernSmooth,
    knitr,
    lifecycle,
    lintr,
    LPSGL,
    matrixStats,
    matrixTests,
    methods,
    mLLMCelltype,
    org.Hs.eg.db,
    pak,
    patchwork,
    PIPET,
    plyr,
    preprocessCore,
    processx,
    qs2,
    randomcoloR,
    RColorBrewer,
    remotes,
    reticulate,
    rmarkdown,
    rSIDISH (>= 0.0.2),
    rstudioapi,
    rTiRank,
    scCustomize,
    SCIPAC,
    scPAS,
    ScPP,
    SingleR,
    sparseMatrixStats,
    testthat (>= 3.0.0),
    tibble,
    tictoc,
    tidycheckUsage,
    tidyr,
    WGCNA,
    zeallot
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true