diffcyt

DOI: 10.18129/B9.bioc.diffcyt    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see diffcyt.

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

Bioconductor version: 3.12

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 <lukas.weber.edu at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("diffcyt")

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("diffcyt")

 

HTML	R Script	diffcyt workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software
Version	1.10.0
In Bioconductor since	BioC 3.7 (R-3.5) (3 years)
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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
SystemRequirements
Enhances
URL	https://github.com/lmweber/diffcyt
BugReports	https://github.com/lmweber/diffcyt/issues
Depends On Me	cytofWorkflow
Imports Me
Suggests Me	CATALYST, HDCytoData
Links To Me
Build Report

Package Archives

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

Source Package	diffcyt_1.10.0.tar.gz
Windows Binary	diffcyt_1.10.0.zip
macOS 10.13 (High Sierra)	diffcyt_1.10.0.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	https://bioconductor.org/packages/diffcyt/
Package Downloads Report	Download Stats