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openCyto

Hierarchical Gating Pipeline for flow cytometry data


Bioconductor version: Release (3.18)

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")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.14.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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
System Requirements
URL
See More
Suggests flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS
Linking To cpp11, BH
Enhances
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto
Links To Me
Build Report Build Report

Package Archives

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

Source Package openCyto_2.14.0.tar.gz
Windows Binary openCyto_2.14.0.zip
macOS Binary (x86_64) openCyto_2.14.0.tgz
macOS Binary (arm64)
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