Package: cellreportR
Title: Cell Culture Microscopy Assay Analysis and Reporting
Version: 0.2.1.9000
Authors@R: c(
    person("Raban", "Heller",
           email = "raban.heller@charite.de",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0001-8006-9742")),
    person("Leila", "Schwindling", role = "aut"),
    person("Alexander", "Büchner", role = "aut"),
    person("Lucia", "Lindenberger", role = "aut"),
    person("Steffen", "Müller", role = "aut"),
    person("Michael", "Hannemann", role = "aut"),
    person("Gerhard", "Achatz", role = "aut"),
    person("Simone", "Rothmiller", role = "aut"))
Description: Analysis and reporting pipeline for cell culture assays
        read out by microscopy, starting from segmented single-cell
        exports such as those written by 'segmantR', 'CellProfiler' or
        'QuPath'. Recovers the experimental design from the directory
        tree and the file naming convention, resolves acquisitions into
        the analysis unit of replication, and standardizes every cell
        against the control condition of its own batch. Applies
        threshold and biological quality control gates, then estimates
        effect sizes with confidence intervals at both unit and cell
        level so that the cost of treating cells as replicates is
        visible rather than assumed. Sample sizes for a follow-up study
        are solved from the confidence bound nearer the null instead of
        the observed point estimate, after Cohen (1988,
        ISBN:9780805802832). Figures, machine-readable tables and a
        generated file of every quoted number are emitted from the same
        objects, and an interactive 'shiny' application provides guided
        analysis and report export.
License: MIT + file LICENSE
URL: https://github.com/CTTIR/cellreportR,
        https://cttir.github.io/cellreportR/
BugReports: https://github.com/CTTIR/cellreportR/issues
Depends: R (>= 4.1.0)
Imports: cli, digest, dplyr, ggplot2, jsonlite, pROC, readr, readxl,
        rlang, scales, shiny, stats, tibble, tidyr, tools, utils
Suggests: bslib, DT, flowCore, knitr, plotly, rmarkdown, shinytest2,
        shinyWidgets, sva, svglite, testthat (>= 3.0.0), withr, writexl
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
Config/Needs/website: CTTIR/themakR
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libx11-dev
        zlib1g-dev
Repository: https://cttir.r-universe.dev
Date/Publication: 2026-11-04 19:04:12 UTC
RemoteUrl: https://github.com/CTTIR/cellreportR
RemoteRef: HEAD
RemoteSha: 885a8753f220936eb98b851dd2272f10da065417
NeedsCompilation: no
Packaged: 2026-11-04 22:06:17 UTC; root
Author: Raban Heller [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-8006-9742>),
  Leila Schwindling [aut],
  Alexander Büchner [aut],
  Lucia Lindenberger [aut],
  Steffen Müller [aut],
  Michael Hannemann [aut],
  Gerhard Achatz [aut],
  Simone Rothmiller [aut]
Maintainer: Raban Heller <raban.heller@charite.de>