CytoML

DOI: 10.18129/B9.bioc.CytoML    

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: Release (3.12)

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 <wjiang2 at fhcrc.org>, Jake Wagner <jpwagner at fhcrc.org>

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

Installation

To install this package, start R (version "4.0") 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 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 2.2.1
In Bioconductor since BioC 3.4 (R-3.3) (4 years)
License file LICENSE
Depends R (>= 3.5.0)
Imports cytolib(>= 2.1.18), flowCore(>= 1.99.10), flowWorkspace(>= 4.1.8), openCyto(>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, lattice, stats, corpcor, RUnit, tibble, RcppParallel, xml2
LinkingTo Rcpp, BH (>= 1.62.0-1), RProtoBufLib, cytolib( >= 1.99.26), Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1), flowWorkspace
Suggests testthat, flowWorkspaceData, 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 FlowSOM
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_2.2.1.tar.gz
Windows Binary CytoML_2.2.1.zip
macOS 10.13 (High Sierra) CytoML_2.2.1.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
Old Source Packages for BioC 3.12 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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