openCyto

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

Hierarchical Gating Pipeline for flow cytometry data

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DOI: 10.18129/B9.bioc.openCyto

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software

Version 2.22.0

In Bioconductor since BioC 2.13 (R-3.0) (12 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

Links To Me

Build Report Build Report

Package Archives

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

Source Package openCyto_2.22.0.tar.gz

Windows Binary (x86_64) openCyto_2.22.0.zip

macOS Binary (x86_64) openCyto_2.22.0.tgz

macOS Binary (arm64) openCyto_2.22.0.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/

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