DESCRIPTION

Package: OOSAP
Type: Package
Title: OHSU-ONPRC Single-cell Analysis Package
Version: 0.1.1
Author: Bimber Lab
Maintainer: The package maintainer <mahyarie@ohsu.edu>
Description: The goal of this package is bringing together tools and pipelines for the analysis of single-cell RNASeq data.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.5.0)
Imports:
    Seurat,
    Rlabkey,
    data.table,
    dplyr,
    tidyr,
    naturalsort,
    DropletUtils,
    Matrix,
    ggplot2,
    cowplot,
    cluster,
    knitr,
    fitdistrplus,
    Hmisc,
    RColorBrewer,
    methods,
    monocle,
    rpart,
    rpart.plot,
    reticulate,
    garnett,
    glmnet,
    ranger,
    org.Hs.eg.db,
    org.Mm.eg.db,
    fastAdaboost,
    caret,
    scater,
    SingleR,
    biomaRt,
    DESeq2,
    MAST,
    kernlab,
    Biostrings,
    KernSmooth,
    BiocGenerics,
    RDAVIDWebService,
    STRINGdb,
    stringr,
    reshape2,
    patchwork,
    Rtsne,
    scales,
    SummarizedExperiment,
    shiny,
    kableExtra (>= 1.2.0),
    DT,
    destiny,
    gtools,
    ggbeeswarm,
    celldex
Suggests:
    ggvis,
    devtools,
    testthat (>= 2.1.0)
Remotes:
    cole-trapnell-lab/garnett,
    bioc::release/DropletUtils,
    bioc::release/DESeq2,
    bioc::release/MAST,
    bioc::release/celldex,
    bioc::release/SingleR,
    bioc::release/SummarizedExperiment,
    bioc::release/RDAVIDWebService,
    bioc::release/STRINGdb
RoxygenNote: 7.1.1
Collate: 
    'Utils.R'
    'Classification_Caret.R'
    'Classification_Garnett.R'
    'Classification_MCE.R'
    'Classification_SGS.R'
    'Classification_Sim.R'
    'GeneAliasing.R'
    'GeneNames.R'
    'LabKeySettings.R'
    'Monocle_III.R'
    'PhenotypingGeneSets.R'
    'PseudoBulk.R'
    'Seurat_III.R'
    'SingleR_Seurat.R'
    'Viz.R'
    'data.R'
    'mcl.R'
    'plotDiffusionMaps.R'
    'postSDA_processing.R'