DESCRIPTION

Package: SPEEDI
Title: Single-cell Pipeline for End to End Data Integration (SPEEDI)
Version: 1.2.1.0000
Authors@R: c(
    person("Yuan", "Wang", email = "yuanwang@princeton.edu", role = c("aut", "cre")),
    person("William", "Thistlethwaite", email = "wat2@princeton.edu", role = "aut"))
Description: To facilitate single cell omics dataset integration and improve reproducibility, we introduce SPEEDI (Single-cell Pipeline for End to End Data Integration), an automated end-to-end tool package for batch label inference, data integration and cell type labeling.
License: non-commercial LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
LazyData: true
Imports: 
    Azimuth,
    BiocGenerics,
    BiocManager,
    Biostrings,
    bluster,
    chromVAR,
    ComplexHeatmap,
    DESeq2,
    doParallel,
    digest,
    dplyr,
    foreach,
    edgeR,
    GenomicRanges,
    glmGamPoi,
    ggplot2,
    hdf5r,
    hexbin,
    httr,
    jsonlite,
    kneedle,
    limma,
    lisi,
    logr,
    Matrix,
    motifmatchr,
    outliers,
    parallel,
    pheatmap,
    RCurl,
    rhdf5,
    Rsamtools,
    S4Vectors,
    scDblFinder,
    Seurat,
    SeuratData,
    SeuratDisk,
    SeuratObject,
    Signac,
    stringr,
    SummarizedExperiment,
    uwot
Depends: 
    utils,
    logr,
    ArchR
Remotes: 
    github::GreenleafLab/ArchR,
    github::immunogenomics/harmony,
    github::bwlewis/irlba,
    github::etam4260/kneedle,
    github::neurorestore/Libra,
    github::immunogenomics/lisi,
    github::mojaveazure/seurat-disk,
    github::satijalab/seurat-data,
    github::satijalab/azimuth,
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown
VignetteBuilder: knitr