CytoML

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CytoML.

A GatingML Interface for Cross Platform Cytometry Data Sharing


Bioconductor version: 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 (!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")
How to export a GatingSet to GatingML HTML R Script
How to import Cytobank into a GatingSet HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements xml2, GNU make, C++11
URL https://github.com/RGLab/CytoML
Bug Reports https://github.com/RGLab/CytoML/issues
See More
Suggests testthat, flowWorkspaceData(>= 2.11.1), knitr, parallel
Linking To Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel
Enhances
Depends On Me
Imports Me
Suggests Me flowWorkspace, openCyto
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/CytoML/
Package Short Url https://bioconductor.org/packages/CytoML/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive