CytoML
This is the released version of CytoML; for the devel version, see CytoML.
A GatingML Interface for Cross Platform Cytometry Data Sharing
Bioconductor version: Release (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("CytoML")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.24.0 |
| 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 |
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_2.24.0.tar.gz |
| Windows Binary (x86_64) | CytoML_2.24.0.zip |
| macOS Binary (big-sur-x86_64) | CytoML_2.24.0.tgz |
| macOS Binary (sonoma-arm64) | CytoML_2.24.0.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/ |
| Package Downloads Report | Download Stats |