diffcyt

This is the released version of diffcyt; for the devel version, see diffcyt.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-3282-1730

Maintainer: Lukas M. Weber <weberlm3 at gmail.com>

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

Lukas M. Weber. diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. doi:10.18129/B9.bioc.diffcyt, R package version 1.32.1, https://bioconductor.org/packages/diffcyt.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software
Version	1.32.1
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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

Suggests	BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
Linking To
Enhances
Depends On Me	censcyt, cytofWorkflow
Imports Me	CyTOFpower, treeclimbR, treekoR
Suggests Me	CATALYST, tidytof
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	diffcyt_1.32.1.tar.gz
Windows Binary (x86_64)	diffcyt_1.32.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	diffcyt_1.32.1.tgz
macOS Binary (sonoma-arm64)	diffcyt_1.32.1.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
Old Source Packages for BioC 3.23	Source Archive