CytoML

This is the development version of CytoML; for the stable release version, see CytoML.

A GatingML Interface for Cross Platform Cytometry Data Sharing

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DOI: 10.18129/B9.bioc.CytoML

Bioconductor version: Development (3.23)

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 <mike at ozette.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

flowJo parser HTML R Script

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software

Version 2.23.0

In Bioconductor since BioC 3.4 (R-3.3) (9 years)

License AGPL-3.0-only

Depends R (>= 3.5.0)

Imports cytolib(>= 2.3.10), flowCore(>= 1.99.10), flowWorkspace(>= 4.1.8), openCyto(>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, stats, tibble

System Requirements xml2, GNU make, C++11

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

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

Suggests testthat, flowWorkspaceData, knitr, rmarkdown, parallel

Linking To cpp11, BH (>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace

Enhances

Depends On Me

Imports Me

Suggests Me FlowSOM, 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_2.23.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) CytoML_2.23.0.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/

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