CytoML

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CytoML.

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: 3.10

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>

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software

Version 1.12.1

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License Artistic-2.0

Depends

Imports flowCore(>= 1.43.10), flowWorkspace(>= 3.33.10), openCyto(>= 1.11.3), XML, data.table, jsonlite, RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, lattice, stats, corpcor, RUnit

System Requirements xml2, GNU make, C++11

URL https://github.com/RGLab/CytoML

Bug Reports https://github.com/RGLab/CytoML/issues

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 FlowSOM

Suggests Me flowWorkspace, openCyto

Links To Me

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