OSTA/DESCRIPTION at devel · lmweber/OSTA · GitHub

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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: 1.3.0
Date: 2026-03-11
Authors@R:
    c(person("Helena L.", "Crowell",
             role=c("aut"),
             email = "helena@crowell.eu",
             comment = c(ORCID = "0000-0002-4801-1767")),
      person("Mark D.", "Robinson",
             role = c("aut"),
             email = "mark.robinson@mls.uzh.ch",
             comment = c(ORCID = "0000-0002-3048-5518")),
      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/issues
biocViews:
    Spatial,
    SingleCell,
    GeneExpression,
    Transcriptomics
Depends:
    R (>= 4.5)
Imports:
    anndataR,
    AUCell,
    Banksy,
    basilisk,
    BayesSpace,
    BiocFileCache,
    BiocParallel,
    CARDspa,
    DESpace,
    doMC,
    dplyr,
    DropletUtils,
    EBImage,
    ExperimentHub,
    GenomeInfoDb,
    ggfortify,
    ggplot2,
    ggrepel,
    ggspavis,
    harmony,
    hoodscanR,
    igraph,
    imcdatasets,
    imcRtools,
    jsonlite,
    lme4,
    lmerTest,
    msigdbr,
    muSpaData,
    nnSVG,
    openxlsx,
    osfr,
    OSTA.data,
    pals,
    patchwork,
    pheatmap,
    RANN,
    RColorBrewer,
    reticulate,
    rtracklayer,
    scales,
    scater,
    scider,
    scran,
    scuttle,
    scRNAseq,
    sf,
    SFEData,
    SingleR,
    sosta,
    SpaceTrooper,
    spacexr,
    SpatialExperiment,
    SpatialExperimentIO,
    spatialFDA,
    SpatialFeatureExperiment,
    spatialLIBD,
    spatstat,
    spdep,
    spicyR,
    SpotSweeper,
    STexampleData,
    tidyr,
    VisiumIO,
    Voyager,
    zoo
Suggests:
    BiocManager,
    BiocPkgTools,
    BiocStyle,
    BiocVersion,
    CCPlotR,
    downlit,
    glue,
    knitr,
    markdown,
    quarto,
    scrapper,
    sessioninfo,
    Statial,
    xml2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
BiocType: Book
License: CC BY 4.0
VignetteBuilder: knitr
BiocBookTemplate: 1.0.6
SystemRequirements: quarto