DESCRIPTION

Package: SCWorkflow
Title: SCWorkflow from NIDAP
Version: 1.0.2
Authors@R:  c(person("Maggie", "Cam", email = "maggie.cam@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-8190-9766")), 
    person("Thomas", "Meyer", email = "thomas.meyer@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7185-5597")), 
    person("Jing", "Bian", email = "bianjh@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-7109-716X")), 
    person("Alexandra", "Michalowski", email = "michaloa@mail.nih.gov", role = "aut", comment = c(ORCID = "0000-0001-9259-6101")),
    person("Alexei", "Lobanov", email = "alexei.lobanov@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-9883-4374")),
    person("Philip", "Homan", email = "philip.homan@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-3389-4931")),
    person("Rui", "He", email = "rui.he@nih.gov", role = "aut"))
Description: A set of functions for analyzing single-cell RNA-seq data using the
    Seurat workflow. The user provides H5 files containing the results of the
    upstream processing through CellRanger, and the package functions allow for
    the QC, filtering, normalization, annotation, differential gene expression,
    and further visualizations and analysis based on user input. This package can
    be run both in a docker container and in user-friendly web-based interactive
    notebooks (NIDAP, Palantir Foundry).
License: MIT
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: 
    testthat (>= 3.0.0)
Depends:
    R (>= 4.0)
Imports:
    anndata (>= 0.7.5.2),
    callr (>= 3.7.1),
    cowplot (>= 1.1.1),
    data.table (>= 1.14.2),
    dplyr (>= 1.0.9),
    edgeR (>= 3.36.0),
    future.apply (>= 1.9.0),
    future (>= 1.27.0),
    gargle (>= 1.2.0),
    ggplot2 (>= 3.3.6),
    ggpubr (>= 0.4.0),
    globals (>= 0.16.1),
    harmony (>= 0.1.1),
    hdf5r (>= 1.3.5),
    httpuv (>= 1.6.5),
    leiden (>= 0.4.2),
    limma (>= 3.50.3),
    magrittr (>= 2.0.3),
    markdown (>= 1.1),
    methods (>= 4.1.3),
    plotly (>= 4.10.0), 
    progressr (>= 0.10.1),
    pryr (>= 0.1.5),
    purrr (>= 0.3.4),
    quantmod (>= 0.4.20),
    reshape2 (>= 1.4.4),
    reticulate (>= 1.25),
    rlang (>= 1.0.6),
    statmod (>= 1.4.37),
    stringr (>= 1.4.1),
    svglite (>= 2.1.0),
    tibble (>= 3.1.8),
    tidyverse (>= 1.3.2),
    viridisLite (>= 0.4.0),
    xfun (>= 0.32),
    zip (>= 2.2.0),
    ComplexHeatmap (>= 2.10.0),
    MAST (>= 1.20.0),
    SingleR (>= 1.8.1),
    BiocManager,
    gridBase (>= 0.4-7),
    gridExtra (>= 2.3),
    RColorBrewer (>= 1.1-3),
    Seurat (>= 4.1.1),
    gtable (>= 0.3.1),
    digest (>= 0.6.29),
    png,
    httr,
    jsonlite,
    plyr,
    colorspace,
    dendextend,
    dendsort,
    pheatmap,
    scales,
    celldex,
    gdata,
    ggrepel,
    tidyr,
    htmlwidgets,
    scDblFinder
Config/testthat/edition: 3