openCyto

This is the released version of openCyto; for the devel version, see openCyto.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: Release (3.23)

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")):

Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo. openCyto: Hierarchical Gating Pipeline for flow cytometry data. doi:10.18129/B9.bioc.openCyto, R package version 2.24.0, https://bioconductor.org/packages/openCyto.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version	2.24.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 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, grDevices
System Requirements
URL

Suggests	flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats (>= 4.5.2), MASS
Linking To	cpp11, BH (>= 1.62.0-1)
Enhances
Depends On Me
Imports Me	CytoML
Suggests Me	CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto, staRgate
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	openCyto_2.24.0.tar.gz
Windows Binary (x86_64)	openCyto_2.24.0.zip
macOS Binary (big-sur-x86_64)	openCyto_2.24.0.tgz
macOS Binary (sonoma-arm64)	openCyto_2.24.0.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