DepecheR

DOI: 10.18129/B9.bioc.DepecheR    

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

Bioconductor version: Release (3.9)

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>

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

Installation

To install this package, start R (version "3.6") 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
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 1.0.3
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6)
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), BiocParallel(>= 1.16.6)
LinkingTo Rcpp, RcppEigen
Suggests Rtsne, testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DepecheR_1.0.3.tar.gz
Windows Binary DepecheR_1.0.3.zip
Mac OS X 10.11 (El Capitan) DepecheR_1.0.3.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
Old Source Packages for BioC 3.9 Source Archive

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