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>

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