DESCRIPTION

Package: scdrake
Type: Package
Title: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language
Version: 1.6.0
Authors@R:
    c(
      person(
        given = "Jiri",
        family = "Novotny",
        role = c("aut", "cre"),
        email = "jiri.novotny@img.cas.cz",
        comment = c(ORCID = "0000-0003-1338-638X")
      ),
      person(
        given = "Jan",
        family = "Kubovciak",
        role = c("aut"),
        email = "jan.kubovciak@img.cas.cz"
      ),
      person(
        given = "Lucie",
        family = "Pfeiferova",
        role = c("aut"),
        email = "lucie.pfeiferova@img.cas.cz"
      ),
      person(
        given = "Michal",
        family = "Kolar",
        role = c("fnd"),
        email = "kolarmi@img.cas.cz"
      )
    )
Description:
    This pipeline is implemented in the drake Make-like toolkit (https://github.com/ropensci/drake) and
    provides the following steps of scRNA-seq secondary analysis: input quality control, filtering of cells/genes,
    normalization, clustering, cell type annotation, cluster markers, differential expression analysis
    (constrasts -> cluster vs. cluster), integration of multiple samples.
    All main parts are accompanied by rich graphical outputs and HTML reports
    (RMarkdown). Thanks to the drake package, the pipeline is highly reproducible, scalable and efficient, provides easy
    access to all intermediate results, and can be arbitrarily extended as pipeline definitions are abstracted as
    R objects. A command line interface is available to perform the most important actions directly in shell terminal.
License: MIT + file LICENSE
URL: https://github.com/bioinfocz/scdrake, https://bioinfocz.github.io/scdrake
BugReports: https://github.com/bioinfocz/scdrake/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
VignetteBuilder: knitr
biocViews:
    Transcription,
    DifferentialExpression,
    SingleCell,
    Normalization,
    QualityControl,
    Clustering
Imports:
    AnnotationDbi,
    argparser,
    assertthat,
    batchelor,
    BiocGenerics,
    BiocManager,
    BiocParallel,
    BiocSingular,
    bluster,
    celldex,
    cli,
    cluster,
    clustree,
    codetools,
    conflicted,
    cowplot,
    datasets,
    downlit,
    dplyr,
    drake,
    DropletUtils,
    DT,
    ensembldb,
    fs,
    ggplot2,
    ggplotify,
    glmGamPoi,
    glue,
    harmony,
    here,
    htmltools,
    knitr,
    littler,
    igraph,
    janitor,
    kableExtra,
    magrittr,
    Matrix,
    MatrixGenerics,
    methods,
    parallelly,
    patchwork,
    PCAtools,
    purrr,
    readr,
    RhpcBLASctl,
    rlang,
    rmarkdown,
    S4Vectors,
    scales,
    scater,
    scDblFinder,
    scran,
    SC3,
    Seurat,
    SeuratObject,
    sessioninfo,
    SingleCellExperiment,
    SingleR,
    stringi,
    stringr,
    SummarizedExperiment,
    tibble,
    tidyr,
    tidyselect (== 1.1.2),
    usethis,
    utils,
    withr,
    yaml
Remotes:
    gorgitko/SC3
Suggests:
    BiocStyle,
    clustermq (== 0.8.8),
    covr,
    desc,
    emoji,
    future,
    future.callr,
    org.Hs.eg.db,
    pkgdown,
    preferably,
    processx,
    qs,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Config/testthat/start-first: project