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: 1.3.1
Date: 2026-06-11
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 = "weberlm3@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,
        scrapper, 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
Config/pak/sysreqs: libabsl-dev cmake libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libgdal-dev gdal-bin
        libgeos-dev libglpk-dev make libharfbuzz-dev libmagick++-dev
        gsfonts default-jdk libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libtiff-dev libuv1-dev libxml2-dev
        libssl-dev perl libproj-dev python3 libsqlite3-dev
        libudunits2-dev libnode-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-10 22:13:45 UTC
RemoteUrl: https://github.com/bioc/OSTA
RemoteRef: HEAD
RemoteSha: ca9ebaa54a1ea01c8e22b4c684adbfd81e063884
NeedsCompilation: no
Packaged: 2026-10-10 11:54:48 UTC; root
Author: Helena L. Crowell [aut] (ORCID:
    <https://orcid.org/0000-0002-4801-1767>),
  Mark D. Robinson [aut] (ORCID: <https://orcid.org/0000-0002-3048-5518>),
  Stephanie C. Hicks [aut] (ORCID:
    <https://orcid.org/0000-0002-7858-0231>),
  Lukas M. Weber [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3282-1730>)
Maintainer: Lukas M. Weber <weberlm3@gmail.com>