openCyto
Hierarchical Gating Pipeline for flow cytometry data
Bioconductor version: 3.23 · Package version: 2.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("openCyto")Details
| Maintainer | Mike Jiang <mike@ozette.com> |
| Author | Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo |
| License | AGPL-3.0-only |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Package Short Url | https://bioconductor.org/packages/openCyto/ |
Citation
From within R, enter citation("openCyto"):
Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo. openCyto: Hierarchical Gating Pipeline for flow cytometry data. doi:10.18129/B9.bioc.openCyto, R package version 2.24.0, https://bioconductor.org/packages/openCyto.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- An Introduction to the openCyto package
- OpenCyto: How to use different auto gating functions
- How to write a csv gating template
Download
Follow the installation instructions to use this package in your R session.
| Source package | openCyto_2.24.0.tar.gz |
| Windows binary (x86_64) | openCyto_2.24.0.zip |
| macOS binary (arm64) | openCyto_2.24.0.tgz |
| macOS binary (x86_64) | openCyto_2.24.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: methods, Biobase, BiocGenerics, flowCore (>= 1.99.17), flowViz, ncdfFlow (>= 2.11.34), flowWorkspace (>= 3.99.1), flowClust (>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices
LinkingTo: cpp11, BH (>= 1.62.0-1)
Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats (>= 4.5.2), MASS