DESCRIPTION

Package: dseqr
Type: Package
Title: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations
Version: 0.37.0
Authors@R: person("Alex", "Pickering", email="alexvpickering@gmail.com", role=c("cre", "aut"))
BugReports: https://github.com/hms-dbmi/dseqr/issues
URL: https://github.com/hms-dbmi/dseqr
Description: GUI to import and explore single-cell and bulk RNA-seq datasets 
    and run queries to find similar and opposing L1000 and CMAP02 perturbation 
    signatures. Single-cell fastq files can be quantified, imported, QC'ed,
    annotated and integrated. For integrated datasets, 'limma' pseudobulk 
    differential expression results can be explored within the app or downloaded
    along with pathway and differential abundance analyses. Bulk RNA-seq
    fastq files can also be quantified, imported, analysed, and deconvoluted
    using a single-cell dataset. Finally, differential expression analyses from
    bulk and single-cell datasets can be used to find similar and opposing
    CMAP02 and L1000 perturbation signatures.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.1
BiocViews:
SystemRequirements:
  kallisto (0.46.0)
Imports:
    AnnotationDbi (>= 1.48.0),
    Biobase (>= 2.46.0),
    BiocManager,
    batchelor (>= 1.3.9),
    crossmeta,
    cowplot,
    callr,
    celldex,
    dplyr (>= 0.8.3),
    digest,
    DT (>= 0.11),
    DropletUtils(>= 1.6.1),
    data.table (>= 1.12.8),
    dtangle (>= 2.0.9),
    dseqr.data,
    DWLS,
    edgeR (>= 3.28.0),
    fs,
    FNN,
    grr,
    ggplot2 (>= 3.2.1),
    GO.db (>= 3.10.0),
    glmGamPoi,
    hdf5r (>= 1.3.1),
    htmltools,
    htmlwidgets,
    httr,
    harmony (>= 0.1.0),
    HDF5Array,
    igraph (>= 1.2.4.2),
    jsonlite,
    limma (>= 3.40.2),
    magrittr (>= 1.5),
    Matrix,
    MuSiC,
    methods,
    MASS,
    plyr,
    plotly,
    presto,
    picker (>= 0.2.6),
    qs,
    R.utils,
    repel,
    rhandsontable,
    rkal (>= 0.1.12),
    rlang (>= 0.4.3),
    rintrojs (>= 0.2.2),
    scDblFinder,
    scales,
    Seurat,
    SeuratObject,
    SingleCellExperiment,
    SummarizedExperiment,
    S4Vectors,
    shiny (>= 1.4.0),
    shinyBS (>= 0.61),
    shinyjs (>= 1.1),
    shinyWidgets (>= 0.5.0),
    shinydlplot (>= 0.1.0),
    shinypanel (>= 0.1.0),
    SingleR (>= 1.1.6),
    scran (>= 1.14.5),
    stringr,
    stats,
    scater (>= 1.15.12),
    symphony (>= 0.1.0),
    tibble (>= 2.1.3),
    tidyr,
    TSP,
    utils
Suggests: 
    testthat (>= 3.0.0),
    scuttle,
    shinytest2
Depends: 
    R (>= 4.1.0)
Remotes: 
    plger/scDblFinder,
    hms-dbmi/dseqr.data,
    hms-dbmi/repel,
    hms-dbmi/picker,
    alexvpickering/rkal,
    alexvpickering/crossmeta,
    alexvpickering/DWLS,
    immunogenomics/presto,
    xuranw/MuSiC
Config/testthat/edition: 3