DESCRIPTION

Package: SCHNAPPs
Type: Package
Title: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Version: 1.15.27
Authors@R: c(person("Bernd", "Jagla", role = c("aut", "cre"), email = "bernd.jagla@pasteur.fr", comment = c(ORCID = "0000-0002-7696-0484")))
Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr>
Description: Single Cell sHiny APPlication (SCHNAPPs) is a R/Shiny based application to interact, manipulate, explore, and analyze single cell RNA-seq experiments, including MARS-seq and others.
    The application is open and extendable. The main idea is to be able to run basic visualization and analyses, including normalization, clustering,...
    on a defined subset of cells/genes. Key is, that all computations are based only on the cells that have been selected. Input can be a 
    SingleCellExperiment object or CSV/TSV files of the count matrix.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: 
    R (>= 3.6)
Imports:
    future,
    doParallel,
    future.callr,
    BPCells,
    BiocParallel,
    purrr,
    DT,
    Matrix,
    shiny,
    shinyTree,
    psychTools,
    pryr,
    colourpicker,
    digest,
    memoise,
    Seurat,
    circlize,
    kohonen,
    scater,
    scran,
    shinyjs,
    tidySingleCellExperiment,
    SingleCellExperiment,
    shinyWidgets,
    ggplotify,
    dendsort,
    reactlog,
    ggpubr,
    dplyr,
    glue,
    evaluate,
    shinydashboard,
    profvis,
    shinydashboardPlus
Remotes: 
    jokergoo/ComplexHeatmap,
    jokergoo/InteractiveComplexHeatmap,
    haowulab/Wind,
    chris-mcginnis-ucsf/DoubletFinder,
    renozao/xbioc,
    Zhangxf-ccnu/scDEA,
    Albluca/distutils,
    Albluca/ElPiGraph.R,
    BaderLab/Tempora,
    RausellLab/CelliD,
    msraredon/Connectome,
    Coolgenome/iTALK,
    nghiavtr/BPSC,
    statOmics/zingeR,
    cysouw/qlcMatrix,
    bnprks/BPCells/r,
    saezlab/liana
Suggests:
    tidyverse,
    ComplexHeatmap,
    reactlog,
    shinythemes,
    pdftools,
    manhattanly,
    ggalluvial,
    pheatmap,
    rmarkdown,
    TRONCO,
    rintrojs,
    shinyAce,
    shinyjqui,
    shinycssloaders,
    DESeq2,
    SIMLR,
    knitr,
    Hmisc,
    orca,
    debugme,
    shinyBS,
    archivist,
    ggnetwork,
    GSEABase,
    GSVA,
    heatmaply,
    kableExtra,
    MAST,
    mclust,
    monocle,
    multtest,
    network,
    pdftools,
    Rsomoclu,
    glmGamPoi,
    rtracklayer,
    scDEA,
    shinytest,
    SingleR,
    spatstat,
    Tempora,
    threejs,
    SingleCellSignalR,
    tidyverse,
    Wind,
    xbioc,
    testthat (>= 3.0.0)
RoxygenNote: 7.3.1
URL: https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs
BugReports: https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/issues
biocViews: Visualization, GUI, DimensionReduction, 
    FeatureExtraction, Clustering, Transcription, 
    GeneExpression, Transcriptomics, SingleCell, CellBasedAssays,
    Sequencing, Coverage, Normalization, ImmunoOncology, DataImport
VignetteBuilder: knitr
Config/testthat/edition: 3