openCyto
This is thereleased version of openCyto; for the devel version, seeopenCyto.
Hierarchical Gating Pipeline for flow cytometry data
Bioconductor version: Release (3.22)
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")BiocManager::install("openCyto")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport,DataRepresentation,FlowCytometry,ImmunoOncology,Preprocessing,Software |
| Version | 2.22.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 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, grDevices |
| 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 (>= 1.62.0-1) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | openCyto_2.22.0.tar.gz |
| Windows Binary (x86_64) | openCyto_2.22.0.zip |
| macOS Binary (x86_64) | openCyto_2.22.0.tgz |
| macOS Binary (arm64) | openCyto_2.22.0.tgz |
| 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 |