Package: standR
Title: Spatial transcriptome analyses of Nanostring's DSP data in R
Version: 1.15.0
Authors@R: 
    c(person(given = "Ning",
             family = "Liu",
             role = c("aut", "cre"),
             email = "ning.liu@adelaide.edu.au",
             comment = c(ORCID = "0000-0002-9487-9305")),
      person(given = "Dharmesh D",
             family = "Bhuva",
             role = c("aut"),
             email = "bhuva.d@wehi.edu.au",
             comment = c(ORCID = "0000-0002-6398-9157")),
      person(given = "Ahmed",
             family = "Mohamed",
             role = c("aut"),
             email = "mohamed.a@wehi.edu.au"))
Description: standR is an user-friendly R package providing functions
        to assist conducting good-practice analysis of Nanostring's
        GeoMX DSP data. All functions in the package are built based on
        the SpatialExperiment object, allowing integration into various
        spatial transcriptomics-related packages from Bioconductor.
        standR allows data inspection, quality control, normalization,
        batch correction and evaluation with informative
        visualizations.
biocViews: Spatial, Transcriptomics, GeneExpression,
        DifferentialExpression, QualityControl, Normalization,
        ExperimentHubSoftware
License: MIT + file LICENSE
URL: https://github.com/DavisLaboratory/standR
BugReports: https://github.com/DavisLaboratory/standR/issues
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment,
        SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2,
        tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics,
        grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr,
        ggrepel, cluster, testthat (>= 3.0.0)
Config/testthat/edition: 3
Depends: R (>= 4.1)
VignetteBuilder: knitr
Config/pak/sysreqs: make libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:16:04 UTC
RemoteUrl: https://github.com/bioc/standR
RemoteRef: HEAD
RemoteSha: 9a7906569b279ee38d614c1297c7d650dccc09be
NeedsCompilation: no
Packaged: 2025-10-30 12:51:06 UTC; root
Author: Ning Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9487-9305>),
  Dharmesh D Bhuva [aut] (ORCID: <https://orcid.org/0000-0002-6398-9157>),
  Ahmed Mohamed [aut]
Maintainer: Ning Liu <ning.liu@adelaide.edu.au>
Built: R 4.6.0; ; 2025-10-30 12:53:41 UTC; windows
