openCyto
Hierarchical Gating Pipeline for flow cytometry data
Bioconductor version: 3.24 · Package version: 2.25.0
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 |
| Downloads rank | 1636 |
| Source branch | devel |
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software |
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_2.25.0.tar.gz |
| Windows binary (x86_64) | openCyto_2.25.0.zip |
| macOS binary (arm64) | openCyto_2.25.0.tgz |
| macOS binary (x86_64) | openCyto_2.25.0.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