CytoML

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: Development (3.24)

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")):

Mike Jiang, Jake Wagner. CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing. doi:10.18129/B9.bioc.CytoML, R package version 2.25.0, https://bioconductor.org/packages/CytoML.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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")

How to import Cytobank into a GatingSet	HTML	R Script
flowJo parser	HTML	R Script
How to export a GatingSet to GatingML	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	2.25.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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++17
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	CyFj11, FlowSOM, flowWorkspace, openCyto
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CytoML_2.25.0.tar.gz
Windows Binary (x86_64)	CytoML_2.25.0.zip
macOS Binary (big-sur-x86_64)	CytoML_2.25.0.tgz
macOS Binary (sonoma-arm64)	CytoML_2.25.0.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