DOI: 10.18129/B9.bioc.diffcyt    

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

Differential discovery in high-dimensional cytometry via high-resolution clustering

Bioconductor version: 3.8

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

Author: Lukas M. Weber [aut, cre]

Maintainer: Lukas M. Weber <lukmweber at gmail.com>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script diffcyt workflow
PDF   Reference Manual
Text   NEWS


biocViews CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software
Version 1.2.23
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License MIT + file LICENSE
Depends R (>= 3.4.0)
Imports flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid
Suggests BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
URL https://github.com/lmweber/diffcyt
BugReports https://github.com/lmweber/diffcyt/issues
Depends On Me
Imports Me
Suggests Me CATALYST
Links To Me
Build Report  

Package Archives

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

Source Package diffcyt_1.2.23.tar.gz
Windows Binary diffcyt_1.2.23.zip
Mac OS X 10.11 (El Capitan) diffcyt_1.2.23.tgz
Source Repository git clone https://git.bioconductor.org/packages/diffcyt
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/diffcyt
Package Short Url http://bioconductor.org/packages/diffcyt/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: