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diffcyt

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
diffcyt workflow HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL https://github.com/lmweber/diffcyt
Bug Reports https://github.com/lmweber/diffcyt/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
Linking To
Enhances
Depends On Me censcyt, cytofWorkflow
Imports Me CyTOFpower, treekoR
Suggests Me CATALYST
Links To Me
Build Report Build Report

Package Archives

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

Source Package diffcyt_1.22.0.tar.gz
Windows Binary diffcyt_1.22.0.zip
macOS Binary (x86_64) diffcyt_1.22.0.tgz
macOS Binary (arm64) diffcyt_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/diffcyt
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/diffcyt
Bioc Package Browser https://code.bioconductor.org/browse/diffcyt/
Package Short Url https://bioconductor.org/packages/diffcyt/
Package Downloads Report Download Stats