CytoML
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see CytoML.
A GatingML Interface for Cross Platform Cytometry Data Sharing
Bioconductor version: 3.15
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.ai>
Citation (from within R, enter
citation("CytoML")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software |
| Version | 2.8.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | file LICENSE |
| 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, base64enc, plyr, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, lattice, stats, corpcor, RUnit, tibble, RcppParallel, xml2 |
| 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 | Rcpp, BH (>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1), flowWorkspace |
| Enhances | |
| Depends On Me | |
| Imports Me | FlowSOM |
| Suggests Me | 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_2.8.1.tar.gz |
| Windows Binary | CytoML_2.8.1.zip |
| macOS Binary (x86_64) | CytoML_2.8.1.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |