openCyto

DOI: 10.18129/B9.bioc.openCyto    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: 3.13

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 <wjiang2 at fhcrc.org>,Jake Wagner <jpwagner at fhcrc.org>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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

Details

biocViews	DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version	2.4.0
In Bioconductor since	BioC 2.13 (R-3.0) (8 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	methods, Biobase, BiocGenerics, gtools, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowStats(>= 3.99.1), flowClust(>= 3.11.4), MASS, clue, plyr, RBGL, graph, data.table, ks, RColorBrewer, lattice, rrcov, R.utils
LinkingTo	Rcpp
Suggests	flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML
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_2.4.0.tar.gz
Windows Binary	openCyto_2.4.0.zip
macOS 10.13 (High Sierra)	openCyto_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/openCyto
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/openCyto
Package Short Url	https://bioconductor.org/packages/openCyto/
Package Downloads Report	Download Stats