Package: DepecheR 1.21.3

Jakob Theorell

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

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.

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

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DepecheR.pdf |DepecheR.html✨
DepecheR/json (API)
NEWS

# Install 'DepecheR' in R:
install.packages('DepecheR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • testData - A 14 color flow cytometry dataset for example execution and playing around
  • testDataDepeche - A depeche clustering of the testData set
  • testDataSNE - SNE of the testData set

On BioConductor:DepecheR-1.21.2(bioc 3.20)DepecheR-1.20.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

13 exports 1.38 score 77 dependencies 2 mentions

Last updated 19 days agofrom:2298002365

Exports:dColorPlotdColorVectordContoursdDensityPlotdepechedResidualPlotdScaledSplsdadViolinsdWilcoxgroupProbPlotneighSmoothnUniqueNeighDons

Dependencies:beanplotBHBiocParallelbitopscaToolscliClusterRcodetoolscollapsecolorspacecorpcorcpp11DEoptimRdoSNOWdplyrellipsefansifarverFNNforeachformatRfutile.loggerfutile.optionsgdatagenericsggplot2ggrepelgluegmodelsgmpgplotsgridExtragtablegtoolsigraphisobanditeratorsKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmixOmicsmomentsmunsellnlmepillarpkgconfigplyrpurrrR6rARPACKRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrobustbaseRSpectrascalessnowstringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithr

Example of a cytometry data analysis with DepecheR

Jakob Theorell

Rendered fromDepecheR_test.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2020-06-05
Started: 2019-01-09

Probability plot usage

Jakob Theorell

Rendered fromGroupProbPlot_usage.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-12-05
Started: 2019-12-05