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>
citation("DepecheR")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("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")| Example of a cytometry data analysis with DepecheR | HTML | R Script |
| Using the groupProbPlot plot function for single-cell probability display | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
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) (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) |
| System Requirements | |
| URL |
See More
| Suggests | uwot, reshape2, testthat, knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | flowSpecs |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/DepecheR/ |
| Package Short Url | https://bioconductor.org/packages/DepecheR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |