CytoML

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

A GatingML Interface for Cross Platform Cytometry Data Sharing


Bioconductor version: 3.11

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

Author: Mike Jiang, J. Spidlen., N. Gopalakrishnan, F. Hahne, B. Ellis, R. Gentleman, M. Dalphin, N. Le Meur, B. Purcell

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 (!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
LICENSE Text

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version 2.0.5
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License file LICENSE
Depends R (>= 3.5.0)
Imports cytolib(>= 2.0.3), flowCore(>= 1.99.10), flowWorkspace(>= 3.99.15), 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
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, knitr, parallel
Linking To Rcpp, BH (>= 1.62.0-1), RProtoBufLib, cytolib( >= 2.0.3), Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1), flowWorkspace
Enhances
Depends On Me
Imports Me FlowSOM
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_2.0.5.tar.gz
Windows Binary CytoML_2.0.5.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CytoML_2.0.5.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 3.11 Source Archive