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CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing


Bioconductor version: Release (3.18)

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 "4.3") 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")
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

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version 2.14.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
See More
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_2.14.0.tar.gz
Windows Binary CytoML_2.14.0.zip
macOS Binary (x86_64) CytoML_2.14.0.tgz
macOS Binary (arm64)
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