openCyto

DOI: 10.18129/B9.bioc.openCyto    

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: Release (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>

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

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

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