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openCyto

This is the development version of openCyto; for the stable release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("openCyto")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.15.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License AGPL-3.0-only
Depends
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
Windows Binary
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/openCyto/
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