CytoML

DOI: 10.18129/B9.bioc.CytoML  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CytoML.

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: 3.16

Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

Author: Mike Jiang, Jake Wagner

Maintainer: Mike Jiang <mike at ozette.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("CytoML")

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("CytoML")

 

HTML	R Script	flowJo parser
HTML	R Script	How to export a GatingSet to GatingML
HTML	R Script	How to import Cytobank into a GatingSet
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version	2.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	AGPL-3.0-only
Depends	R (>= 3.5.0)
Imports	cytolib(>= 2.3.10), flowCore(>= 1.99.10), flowWorkspace(>= 4.1.8), openCyto(>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, stats, tibble
LinkingTo	cpp11, BH (>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace
Suggests	testthat, flowWorkspaceData, knitr, rmarkdown, parallel
SystemRequirements	xml2, GNU make, C++11
Enhances
URL	https://github.com/RGLab/CytoML
BugReports	https://github.com/RGLab/CytoML/issues
Depends On Me
Imports Me
Suggests Me	FlowSOM, flowWorkspace, openCyto
Links To Me
Build Report

Package Archives

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

Source Package	CytoML_2.10.0.tar.gz
Windows Binary	CytoML_2.10.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CytoML
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CytoML
Bioc Package Browser	https://code.bioconductor.org/browse/CytoML/
Package Short Url	https://bioconductor.org/packages/CytoML/
Package Downloads Report	Download Stats