openCyto

DOI: 10.18129/B9.bioc.openCyto  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: 3.17

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Author: Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo

Maintainer: Mike Jiang <mike at ozette.com>

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

Installation

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

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

BiocManager::install("openCyto")

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("openCyto")

 

HTML R Script An Introduction to the openCyto package
HTML R Script How to use different auto gating functions
HTML R Script How to write a csv gating template
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.12.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License AGPL-3.0-only
Depends R (>= 3.5.0)
Imports methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer
LinkingTo cpp11, BH
Suggests flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS
SystemRequirements
Enhances
URL
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto
Links To Me
Build Report  

Package Archives

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

Source Package openCyto_2.12.0.tar.gz
Windows Binary openCyto_2.12.0.zip (64-bit only)
macOS Binary (x86_64) openCyto_2.12.0.tgz
macOS Binary (arm64) openCyto_2.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/openCyto
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/openCyto
Bioc Package Browser https://code.bioconductor.org/browse/openCyto/
Package Short Url https://bioconductor.org/packages/openCyto/
Package Downloads Report Download Stats

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