DESCRIPTION

Package: SCP
Type: Package
Title: Single Cell Pipeline
Version: 0.5.6
Author: Hao Zhang
Maintainer: Hao Zhang <haozhang@njmu.edu.cn>
Description: An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: True
LazyDataCompression: xz
Depends:
    R (>= 4.1.0)
biocViews: SingleCell, GeneExpression, SingleCellWorkflow, Visualization, ShinyApps
Imports:
    AnnotationDbi,
    biomaRt,
    BiocParallel,
    circlize,
    clusterProfiler,
    ComplexHeatmap (>= 2.13.0),
    data.table,
    dplyr (>= 1.1.0),
    future,
    future.apply,
    ggnewscale,
    ggplot2 (>= 3.4.0),
    ggrepel,
    ggforce,
    GO.db,
    GOSemSim,
    grDevices,
    grid,
    gtable,
    HDF5Array,
    igraph,
    intrinsicDimension,
    methods,
    mgcv,
    Matrix,
    patchwork,
    pbapply,
    png,
    plotly,
    proxyC,
    R.cache,
    R.utils,
    reshape2,
    reticulate,
    rlang,
    rhdf5,
    scales,
    simplifyEnrichment (>= 1.5.2),
    slingshot,
    Signac,
    Seurat (>= 4.2.0),
    SeuratObject,
    uwot
Suggests:
    AUCell,
    batchelor,
    Biobase,
    BiocGenerics,
    BiocManager,
    concaveman,
    conos,
    covr,
    cowplot,
    dendextend,
    destiny,
    devtools,
    DDRTree,
    e1071,
    ggpubr,
    ggridges,
    ggsignif,
    ggupset,
    ggVennDiagram,
    ggwordcloud,
    glmGamPoi,
    glmpca,
    harmony,
    hexbin,
    htmlwidgets,
    httr,
    metR,
    monocle,
    MatrixGenerics,
    MASS,
    NMF,
    openxlsx,
    org.Hs.eg.db,
    org.Mm.eg.db,
    promises,
    purrr,
    PFAM.db,
    ragg,
    reactome.db,
    renv,
    RcppParallel,
    RcppML,
    scattermore,
    scds,
    scDblFinder,
    scmap,
    sf,
    shiny (>= 1.6.0),
    styler,
    stringr,
    sva,
    symphony,
    S4Vectors,
    SingleR,
    SingleCellExperiment,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    tidyr,
    umap,
    UCell,
    withr
LinkingTo: Rcpp
RoxygenNote: 7.2.3
Config/testthat/edition: 3
URL: https://github.com/zhanghao-njmu/SCP