DESCRIPTION

Package: CellMembrane
Type: Package
Title: A package with high-level wrappers and pipelines for single-cell RNA-seq tools
Version: 1.0.0
Author: Bimber Lab
Maintainer: The package maintainer <bimber@ohsu.edu>
Description: The goal of this package is to provide high-level wrappers and pipelines to process single-cell RNA-seq data.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 4.3.0)
Imports:
    Seurat,
    SeuratObject,
    tidyr,
    dplyr,
    naturalsort,
    Matrix,
    ggplot2,
    patchwork,
    R.utils,
    utils,
    stats,
    reshape2,
    DropletUtils,
    SingleR,
    celldex,
    DESeq2,
    MAST,
    SummarizedExperiment,
    scDblFinder,
    pheatmap,
    ComplexHeatmap,
    methods,
    egg,
    scuttle,
    DT,
    SingleCellExperiment,
    dsb,
    ggnewscale,
    BiocParallel,
    rlang,
    magick,
    pdftools,
    reticulate,
    SoupX,
    hdf5r,
    phytools,
    rentrez,
    RIRA,
    UCell (>= 2.6.0),
    grid,
    ggplotify,
    phateR,
    magrittr,
    edgeR,
    limma,
    future.apply,
    ggrepel,
    SDAtools,
    dropsim,
    RColorBrewer,
    scales,
    clusterProfiler,
    ggforce, 
    compositions, 
    matrixStats,
    RUVSeq,
    lda,
    parallel,
    text2vec, 
    tibble, 
    readr, 
    mlr3verse,
    mlr3,
    glmnet, 
    flexmix,
    jsonlite,
    dbscan,
    geometry,
    CSCORE,
    WGCNA,
    escape (>= 1.99.0),
    GSVA (>= 1.51.5),
    dynamicTreeCut, 
    pacman,
    circlize, 
    conover.test, 
    colorspace, 
    forcats,
    presto,
    decoupleR,
    OmnipathR
Suggests:
    devtools,
    testthat (>= 2.1.0),
    knitr,
    rmdformats,
    rmarkdown,
    shiny,
    pkgdown,
    org.Hs.eg.db,
    org.Mmu.eg.db
RoxygenNote: 7.3.2
URL: https://github.com/BimberLabInternal/CellMembrane
BugReports: https://github.com/BimberLabInternal/CellMembrane/issues
Remotes:
    niaid/dsb,
    bimberlab/RIRA,
    marchinilab/SDAtools,
    marchinilab/dropsim,
    drisso/RUVSeq,
    carmonalab/UCell,
    davidcsterratt/geometry/pkg,
    ChangSuBiostats/CS-CORE,
    ncborcherding/escape,
    rcastelo/GSVA,
    immunogenomics/presto
Config/reticulate:
  list(
    packages = list(
      list(package = "phate"),
      list(package = "sctour")
    )
  )
Collate: 
    'Analysis.R'
    'CSCore.R'
    'Preprocessing.R'
    'Utils.R'
    'CiteSeq.R'
    'CoNGA.R'
    'Doublets.R'
    'LDA.R'
    'Phate.R'
    'PseudoBulk.R'
    'SDA.R'
    'SeuratUtils.R'
    'Seurat_III.R'
    'SingleR_Seurat.R'
    'Spatial.R'
    'data.R'
    'decoupleR.R'
    'escape.R'
    'sctour.R'
VignetteBuilder: knitr