openCyto

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data


Bioconductor version: 3.11

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 "4.0") 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

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.0.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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
System Requirements
URL
See More
Suggests flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML
Linking To Rcpp
Enhances
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, 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_2.0.0.tar.gz
Windows Binary openCyto_2.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) openCyto_2.0.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive