diffcyt

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see diffcyt.

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


Bioconductor version: 3.7

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on (i) high-resolution clustering and (ii) empirical Bayes moderated tests adapted from transcriptomics.

Author: Lukas M. Weber [aut, cre]

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

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

Installation

To install this package, start R (version "3.5") 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

Details

biocViews CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, Proteomics, SingleCell, Software
Version 1.0.10
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends R (>= 3.5.0)
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
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Suggests BiocStyle, knitr, rmarkdown, HDCytoData, CATALYST
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Package Archives

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

Source Package diffcyt_1.0.10.tar.gz
Windows Binary diffcyt_1.0.10.zip
Mac OS X 10.11 (El Capitan) diffcyt_1.0.10.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
Old Source Packages for BioC 3.7 Source Archive