CytoPipeline

DOI: 10.18129/B9.bioc.CytoPipeline  

Automation and visualization of flow cytometry data analysis pipelines

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	FlowCytometry, ImmunoOncology, Preprocessing, QualityControl, Software, Visualization, WorkflowStep
Version	1.0.2
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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
LinkingTo
Suggests	testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://uclouvain-cbio.github.io/CytoPipeline
BugReports	https://github.com/UCLouvain-CBIO/CytoPipeline/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CytoPipeline_1.0.2.tar.gz
Windows Binary	CytoPipeline_1.0.2.zip (64-bit only)
macOS Binary (x86_64)	CytoPipeline_1.0.2.tgz
macOS Binary (arm64)	CytoPipeline_1.0.2.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
Old Source Packages for BioC 3.17	Source Archive