Package: singleCellTK
Type: Package
Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
Version: 2.2.0
Authors@R: c(person(given="David", family="Jenkins", email="dfj@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0002-7451-4288")),
             person(given="Vidya", family="Akavoor", email="vidyaap@bu.edu", role=c("aut")),
             person(given="Salam", family="Alabdullatif", email="salamha@bu.edu", role=c("aut")),
             person(given="Shruthi", family="Bandyadka", email="sbandya@bu.edu", role=c("aut")),
             person(given="Emma", family="Briars", email="ebriars@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0001-9350-5523")),
             person(given="Xinyun", family="Cao", email="xcao19@bu.edu", role=c("aut")),
             person(given="Sebastian", family="Carrasco Pro", email="abild@coh.org", role=c("aut")),
             person(given="Tyler", family="Faits", email="tfaits@bu.edu", role=c("aut")),
             person(given="Rui", family="Hong", email="rzhong@bu.edu", role=c("aut")),
             person(given=c("Mohammed", "Muzamil"), family="Khan", email="mmkhan@bu.edu", role=c("aut")),
             person(given="Yusuke", family="Koga", email="ykoga07@bu.edu", role=c("aut", "cre")),
             person(given="Anastasia", family="Leshchyk", email="aleshchk@bu.edu", role=c("aut")),
             person(given="Irzam", family="Sarfraz", email="irzam9095@gmail.com", role=c("aut")),
             person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut")),
             person(given="Zhe", family="Wang", email="zhe@bu.edu", role=c("aut")),
             person(given=c("W.", "Evan"), family="Johnson", email="wej@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0002-6247-6595")),
             person(given=c("Joshua", "David"), family="Campbell", email="camp@bu.edu", role=c("aut")))
Depends:
    R (>= 4.0),
    SummarizedExperiment,
    SingleCellExperiment,
    DelayedArray,
    Biobase
Description: Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: SingleCell, GeneExpression, DifferentialExpression, Alignment,
    Clustering, ImmunoOncology
LazyData: TRUE
Imports:
    ape,
    batchelor,
    BiocParallel,
    celldex,
    colourpicker,
    colorspace,
    cowplot,
    cluster,
    ComplexHeatmap,
    data.table,
    DelayedMatrixStats,
    DESeq2,
    dplyr,
    DT,
    ExperimentHub,
    fields,
    ggplot2,
    ggplotify,
    ggrepel,
    ggtree,
    gridExtra,
    GSVA (>= 1.26.0),
    GSVAdata,
    igraph,
    KernSmooth,
    limma,
    MAST,
    Matrix,
    matrixStats,
    methods,
    msigdbr,
    multtest,
    plotly,
    RColorBrewer,
    ROCR,
    Rtsne,
    S4Vectors,
    scater,
    scMerge (>= 1.2.0),
    scran,
    Seurat (>= 3.1.3),
    shiny,
    shinyjs,
    SingleR,
    sva,
    reshape2,
    AnnotationDbi,
    shinyalert,
    circlize,
    enrichR,
    celda,
    shinycssloaders,
    uwot,
    DropletUtils,
    scds (>= 1.2.0),
    reticulate (>= 1.14),
    tools,
    tximport,
    fishpond,
    withr,
    GSEABase,
    R.utils,
    zinbwave,
    scRNAseq (>= 2.0.2),
    TENxPBMCData,
    yaml,
    rmarkdown,
    magrittr,
    scDblFinder,
    metap
RoxygenNote: 7.1.1
Suggests:
    testthat,
    Rsubread,
    BiocStyle,
    knitr,
    lintr,
    xtable,
    spelling,
    org.Mm.eg.db,
    stringr,
    kableExtra,
    shinythemes,
    shinyBS,
    shinyjqui,
    shinyWidgets,
    shinyFiles,
    BiocGenerics
VignetteBuilder: knitr
URL: https://compbiomed.github.io/sctk_docs/
BugReports: https://github.com/compbiomed/singleCellTK/issues
Language: en-US