openCyto
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see openCyto.
Hierarchical Gating Pipeline for flow cytometry data
Bioconductor version: 3.11
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 <wjiang2 at fhcrc.org>,Jake Wagner <jpwagner at fhcrc.org>
citation("openCyto")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | methods, Biobase, BiocGenerics, gtools, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowStats(>= 3.99.1), flowClust(>= 3.11.4), MASS, clue, plyr, RBGL, graph, data.table, ks, RColorBrewer, lattice, rrcov, R.utils |
| System Requirements | |
| URL |
See More
| Suggests | flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | CytoML |
| Suggests Me | CATALYST, flowClust, flowCore, flowStats, 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_2.0.0.tar.gz |
| Windows Binary | openCyto_2.0.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | openCyto_2.0.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |