Package: phenoscapR
Title: Read, Analyse, and Visualise Single-Cell Spatial Biology Data
Version: 0.2.0.9001
Authors@R: c(
    person("R.", "Heller", email = "raban.heller@uni-ulm.de",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0001-8006-9742",
                       affiliation = "Ulm University")),
    person("E.", "Chteinberg", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0002-9231-9291",
                       affiliation = "Ulm University")),
    person("H.", "Witte", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0001-5767-7125",
                       affiliation = "Ulm University")))
Description: Tools for importing, processing, analysing, and
        visualising single-cell spatial biology data from multiplexed
        imaging platforms. Supports cell-table quality control, marker
        normalisation, phenotype summaries, spatial neighbourhood
        statistics such as Ripley's K function (Ripley (1977)
        <doi:10.1111/j.2517-6161.1977.tb01615.x>) and Moran's I (Moran
        (1950) <doi:10.2307/2332142>), and explicit sample and
        coordinate-frame registries. Patient-level inference enumerates
        label allocations for declared contrasts (exact permutation
        tests; Pitman (1937) <doi:10.2307/2984124>) and retains
        unavailable hypotheses when adjusting for multiple testing.
        Grouped summaries expose missingness, eligibility, and
        denominator provenance. Optional canonical cell-table import
        uses 'cellspecR' <https://github.com/CTTIR/cellspecR>; optional
        Self-Organising Nebulous Growths (SONG) embeddings (Senanayake
        et al. (2021) <doi:10.1109/TNNLS.2020.3023941>) use 'songR'
        <https://github.com/CTTIR/songR>. Both optional packages are
        available from <https://cttir.r-universe.dev>.
License: MIT + file LICENSE
URL: https://github.com/CTTIR/phenoscapR,
        https://cttir.github.io/phenoscapR/
BugReports: https://github.com/CTTIR/phenoscapR/issues
Additional_repositories: https://cttir.r-universe.dev
Depends: R (>= 4.1.0)
Imports: data.table, dbscan, digest, ggplot2 (>= 3.0.0), methods,
        stats, utils, grDevices, grid, png
Suggests: brand.yml, bsicons, bslib (>= 0.9.0), cellspecR (>= 1.1.0),
        chromote, deldir, ggtext, gridtext, isoband, jsonlite, knitr,
        mclust, Matrix, RANN, ragg, reactable, rmarkdown, Rtsne,
        S4Vectors, sass, Seurat, SeuratObject, sf, shiny (>= 1.6.0),
        shinytest2, songR, SpatialExperiment, SummarizedExperiment,
        testthat (>= 3.0.0), thematic, uwot, withr
Config/Needs/check: CTTIR/cellspecR, CTTIR/songR
Config/Needs/coverage: covr, CTTIR/cellspecR, CTTIR/songR
Config/Needs/lint: CTTIR/cellspecR, CTTIR/songR
Config/testthat/edition: 3
Config/Needs/website: CTTIR/themakR, pkgdown, CTTIR/cellspecR,
        CTTIR/songR
Encoding: UTF-8
LazyData: true
Language: en-GB
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libpng-dev
Repository: https://cttir.r-universe.dev
Date/Publication: 2026-11-03 15:14:48 UTC
RemoteUrl: https://github.com/CTTIR/phenoscapR
RemoteRef: HEAD
RemoteSha: 72fb1bc9bccf210393071c7a1e2e4a4bb0f552a0
NeedsCompilation: no
Packaged: 2026-11-03 18:17:23 UTC; root
Author: R. Heller [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-8006-9742>, affiliation: Ulm
    University),
  E. Chteinberg [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-9231-9291>, affiliation: Ulm
    University),
  H. Witte [aut, cph] (ORCID: <https://orcid.org/0000-0001-5767-7125>,
    affiliation: Ulm University)
Maintainer: R. Heller <raban.heller@uni-ulm.de>