openCyto
This is the development version of openCyto; for the stable release version, see openCyto.
Hierarchical Gating Pipeline for flow cytometry data
Bioconductor version: Development (3.21)
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
Author: Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo
Maintainer: Mike Jiang <mike at ozette.com>
Citation (from within R, enter
citation("openCyto")):
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("openCyto")
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("openCyto")| An Introduction to the openCyto package | HTML | R Script |
| How to use different auto gating functions | HTML | R Script |
| How to write a csv gating template | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Version | 2.19.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (11 years) |
| License | AGPL-3.0-only |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS |
| Linking To | cpp11, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | CytoML |
| Suggests Me | CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | openCyto_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/openCyto |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/openCyto |
| Bioc Package Browser | https://code.bioconductor.org/browse/openCyto/ |
| Package Short Url | https://bioconductor.org/packages/openCyto/ |
| Package Downloads Report | Download Stats |