DESCRIPTION

Package: OSTA
Title: Orchestrating Spatial Transcriptomics Analysis with Bioconductor
Description: This package contains source files for the "Orchestrating Spatial 
    Transcriptomics Analysis with Bioconductor" online book. This book provides 
    interactive examples and discussion on key principles of computational 
    analysis workflows for spatial transcriptomics data using Bioconductor in 
    R. The book contains chapters describing individual analysis steps as well 
    as extended workflows, each with examples including R code and datasets.
Version: 0.99.0
Date: `r date()`
Authors@R: 
    c(person("Helena L.", "Crowell", 
             role=c("aut"), 
             email = "helena@crowell.eu", 
             comment = c(ORCID="0000-0002-4801-1767")), 
      person("Stephanie C.", "Hicks", 
             role = c("aut"), 
             email = "shicks19@jhu.edu", 
             comment = c(ORCID = "0000-0002-7858-0231")), 
      person("Lukas M.", "Weber", 
             role = c("aut", "cre"), 
             email = "lmweb012@gmail.com", 
             comment = c(ORCID = "0000-0002-3282-1730")))
URL: https://github.com/lmweber/OSTA
BugReports: https://github.com/lmweber/OSTA
biocViews: 
    Book, 
    Spatial, 
    SingleCell, 
    GeneExpression, 
    Transcriptomics
Depends: 
    R (>= 4.3)
Imports:
    AUCell,
    Banksy,
    basilisk,
    BayesSpace,
    BiocFileCache, 
    BiocParallel,
    DESpace,
    doMC,
    dplyr, 
    DropletUtils,
    EBImage,
    ExperimentHub, 
    ggplot2, 
    ggspavis, 
    harmony, 
    hoodscanR,
    igraph, 
    imcRtools, 
    jsonlite, 
    lobstr,
    msigdbr,
    nnSVG, 
    openxlsx,
    osfr,
    OSTA.data,
    pals, 
    patchwork, 
    pheatmap, 
    RANN,
    RColorBrewer,
    reticulate,
    rtracklayer, 
    scales, 
    scater, 
    scran,
    scuttle, 
    SFEData,
    SingleR,
    SpaceTrooper,
    spacexr,
    SpatialExperiment, 
    SpatialExperimentIO, 
    spatialFDA,
    SpatialFeatureExperiment, 
    spatialLIBD,
    spatstat,
    spdep,
    STexampleData, 
    tidyr,
    VisiumIO,
    Voyager,
    zellkonverter,
    zoo
Suggests: 
    BiocManager, 
    BiocStyle, 
    doMC,
    BiocVersion, 
    downlit,
    glue, 
    knitr,
    scrapper,
    sessioninfo, 
    xml2
Remotes:
    drisso/SpaceTrooper@devel_spatialBook,
    estellad/SpatialExperimentIO,
    estellad/OSTA.data,
    dmcable/spacexr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
BiocType: Book
License: CC BY 4.0
VignetteBuilder: knitr
BiocBookTemplate: 1.0.6
SystemRequirements: quarto