cydar

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see cydar.

Using Mass Cytometry for Differential Abundance Analyses

Bioconductor version: 3.6

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 <alun at wehi.edu.au>

Maintainer: Aaron Lun <alun at wehi.edu.au>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FlowCytometry, MultipleComparison, Proteomics, SingleCell, Software

Version 1.2.1

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License GPL-3

Depends BiocParallel, SummarizedExperiment

Imports viridis, methods, shiny, graphics, stats, grDevices, S4Vectors, flowCore, Biobase, Rcpp

System Requirements C++11

URL

Suggests ncdfFlow, testthat, BiocGenerics, 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_1.2.1.tar.gz

Windows Binary cydar_1.2.1.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) cydar_1.2.1.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 https://bioconductor.org/packages/cydar/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive