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CytoPipeline

This is the development version of CytoPipeline; for the stable release version, see CytoPipeline.

Automation and visualization of flow cytometry data analysis pipelines


Bioconductor version: Development (3.19)

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.

Author: Philippe Hauchamps [aut, cre] , Laurent Gatto [aut] , Dan Lin [ctb]

Maintainer: Philippe Hauchamps <philippe.hauchamps at uclouvain.be>

Citation (from within R, enter citation("CytoPipeline")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CytoPipeline")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CytoPipeline")
Automation and Visualization of Flow Cytometry Data Analysis Pipelines HTML R Script
Demonstration of the CytoPipeline R package suite functionalities HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FlowCytometry, ImmunoOncology, Preprocessing, QualityControl, Software, Visualization, WorkflowStep
Version 1.3.4
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.3)
Imports methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales
System Requirements
URL https://uclouvain-cbio.github.io/CytoPipeline
Bug Reports https://github.com/UCLouvain-CBIO/CytoPipeline/issues
See More
Suggests testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me CytoPipelineGUI
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CytoPipeline_1.3.4.tar.gz
Windows Binary CytoPipeline_1.3.4.zip
macOS Binary (x86_64) CytoPipeline_1.3.4.tgz
macOS Binary (arm64) CytoPipeline_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CytoPipeline
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoPipeline
Bioc Package Browser https://code.bioconductor.org/browse/CytoPipeline/
Package Short Url https://bioconductor.org/packages/CytoPipeline/
Package Downloads Report Download Stats