diffcyt

DOI: 10.18129/B9.bioc.diffcyt    

This is the development version of diffcyt; for the stable release version, see diffcyt.

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

Bioconductor version: Development (3.17)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("diffcyt")

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

Documentation

PDF		Reference Manual

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software
Version	1.19.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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
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	censcyt, cytofWorkflow
Imports Me	CyTOFpower, treekoR
Suggests Me	CATALYST
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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