diffcyt

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

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

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DOI: 10.18129/B9.bioc.diffcyt

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0002-3282-1730

Maintainer: Lukas M. Weber <lmweb012 at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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 1.30.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

Links To Me

Build Report Build Report

Package Archives

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

Source Package diffcyt_1.30.0.tar.gz

Windows Binary (x86_64) diffcyt_1.29.0.zip

macOS Binary (x86_64) diffcyt_1.30.0.tgz

macOS Binary (arm64) diffcyt_1.30.0.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/

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