DepecheR

DOI: 10.18129/B9.bioc.DepecheR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see DepecheR.

Determination of essential phenotypic elements of clusters in high-dimensional entities

Bioconductor version: 3.13

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

Author: Jakob Theorell [aut, cre], Axel Theorell [aut]

Maintainer: Jakob Theorell <jakob.theorell at ndcn.ox.ac.uk>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("DepecheR")

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("DepecheR")

 

HTML	R Script	Example of a cytometry data analysis with DepecheR
HTML	R Script	Using the groupProbPlot plot function for single-cell probability display
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, Classification, Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, FeatureExtraction, FlowCytometry, ImmunoOncology, RNASeq, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics(>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1)
LinkingTo	Rcpp, RcppEigen
Suggests	uwot, reshape2, testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	flowSpecs
Links To Me
Build Report

Package Archives

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

Source Package	DepecheR_1.8.0.tar.gz
Windows Binary	DepecheR_1.8.0.zip (64-bit only)
macOS 10.13 (High Sierra)	DepecheR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DepecheR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DepecheR
Package Short Url	https://bioconductor.org/packages/DepecheR/
Package Downloads Report	Download Stats