cydar

DOI: 10.18129/B9.bioc.cydar    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see cydar.

Using Mass Cytometry for Differential Abundance Analyses

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews FlowCytometry, ImmunoOncology, MultipleComparison, Proteomics, SingleCell, Software
Version 1.6.1
In Bioconductor since BioC 3.5 (R-3.4) (2 years)
License GPL-3
Depends BiocParallel, SingleCellExperiment
Imports viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp, BiocNeighbors, SummarizedExperiment
LinkingTo Rcpp
Suggests ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package cydar_1.6.1.tar.gz
Windows Binary cydar_1.6.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cydar_1.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/cydar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cydar
Package Short Url http://bioconductor.org/packages/cydar/
Package Downloads Report Download Stats

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