cydar

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cydar.

Using Mass Cytometry for Differential Abundance Analyses


Bioconductor version: 3.9

Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("cydar")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cydar")

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("cydar")
Detecting differentially abundant subpopulations in mass cytometry data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FlowCytometry, ImmunoOncology, MultipleComparison, Proteomics, SingleCell, Software
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends BiocParallel, SingleCellExperiment
Imports viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp, BiocNeighbors, SummarizedExperiment
System Requirements C++11
URL
See More
Suggests ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cydar_1.8.0.tar.gz
Windows Binary cydar_1.8.0.zip
Mac OS X 10.11 (El Capitan) cydar_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cydar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cydar
Bioc Package Browser https://code.bioconductor.org/browse/cydar/
Package Short Url https://bioconductor.org/packages/cydar/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive