CytoML
This is the development version of CytoML; for the stable release version, see CytoML.
A GatingML Interface for Cross Platform Cytometry Data Sharing
Bioconductor version: Development (3.21)
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 "4.5") 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 |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software |
| Version | 2.19.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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_2.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |