Package: CytoPipeline
Title: Automation and visualization of flow cytometry data analysis
        pipelines
Version: 1.11.1
Authors@R: 
    c(person(given = "Philippe",
             family = "Hauchamps",
             role = c("aut", "cre"),
             email = "philippe.hauchamps@uclouvain.be",
             comment = c(ORCID = "0000-0003-2865-1852")),
      person(given = "Laurent", family = "Gatto",
             email = "laurent.gatto@uclouvain.be",
             role = "aut",
             comment = c(ORCID = "0000-0002-1520-2268")),
      person(given = "Dan",
             family = "Lin",
             role = "ctb",
             email = "dan.8.lin@gsk.com"))
Description: This package provides support for automation and
        visualization of flow cytometry data analysis pipelines. In the
        current state, the package focuses on the preprocessing and
        quality control part. The framework is based on two main S4
        classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline
        steps are linked to corresponding R functions - that are either
        provided in the CytoPipeline package itself, or exported from a
        third party package, or coded by the user her/himself. The
        processing steps need to be specified centrally and explicitly
        using either a json input file or through step by step creation
        of a CytoPipeline object with dedicated methods. After having
        run the pipeline, obtained results at all steps can be
        retrieved and visualized thanks to file caching (the running
        facility uses a BiocFileCache implementation). The package
        provides also specific visualization tools like pipeline
        workflow summary display, and 1D/2D comparison plots of
        obtained flowFrames at various steps of the pipeline.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
BugReports: https://github.com/UCLouvain-CBIO/CytoPipeline/issues
URL: https://uclouvain-cbio.github.io/CytoPipeline
biocViews: FlowCytometry, Preprocessing, QualityControl, WorkflowStep,
        ImmunoOncology, Software, Visualization
Collate: 'CytoPipeline-functions.R' 'CytoPipeline-package.R'
        'CytoPipelineClass.R' 'CytoProcessingStep.R'
        'CytoProcessingStepImplementations.R' 'data.R' 'gating.R'
        'utils.R' 'ggplots.R'
Depends: R (>= 4.4)
Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1),
        ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI,
        diagram, jsonlite, scales
Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
        BiocStyle, reshape2, dplyr, CytoPipelineGUI
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-01-14 13:56:36 UTC
RemoteUrl: https://github.com/bioc/CytoPipeline
RemoteRef: HEAD
RemoteSha: d2d9d72ac2dbbe8073b58975454bbce9bbe3ea81
NeedsCompilation: no
Packaged: 2026-01-15 03:36:53 UTC; root
Author: Philippe Hauchamps [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2865-1852>),
  Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>),
  Dan Lin [ctb]
Maintainer: Philippe Hauchamps <philippe.hauchamps@uclouvain.be>
Built: R 4.6.0; ; 2026-01-15 03:38:38 UTC; windows
