CytoML

DOI: 10.18129/B9.bioc.CytoML    

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: Release (3.9)

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

Author: Mike Jiang

Maintainer: Mike Jiang <wjiang2 at fhcrc.org>

Citation (from within R, enter citation("CytoML")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 How to export a GatingSet to GatingML
HTML R Script How to import Cytobank into a GatingSet
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (3 years)
License Artistic-2.0
Depends
Imports flowCore(>= 1.43.10), flowWorkspace(>= 3.31.17), openCyto(>= 1.11.3), XML, data.table, flowUtils(>= 1.35.7), jsonlite, RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, lattice
LinkingTo Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel
Suggests testthat, flowWorkspaceData(>= 2.11.1), knitr, 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 flowWorkspace, openCyto
Links To Me
Build Report  

Package Archives

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

Source Package CytoML_1.10.0.tar.gz
Windows Binary CytoML_1.10.0.zip
Mac OS X 10.11 (El Capitan) CytoML_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CytoML
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoML
Package Short Url https://bioconductor.org/packages/CytoML/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: