Package: scDD 1.37.0

Keegan Korthauer

scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

Authors:Keegan Korthauer [cre, aut]

scDD_1.37.0.tar.gz
scDD_1.37.0.zip(r-4.7)scDD_1.37.0.zip(r-4.6)scDD_1.37.0.zip(r-4.5)
scDD_1.37.0.tgz(r-4.6-any)scDD_1.37.0.tgz(r-4.5-any)
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scDD_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
scDD/json (API)
NEWS

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

Bug tracker:https://github.com/kdkorthauer/scdd/issues

Datasets:

On BioConductor:scDD-1.37.0(bioc 3.24)scDD-1.36.0(bioc 3.23)

immunooncologybayesianclusteringrnaseqsinglecellmultiplecomparisonvisualizationdifferentialexpression

8.15 score 35 stars 54 scripts 584 downloads 16 mentions 6 exports 106 dependencies

Last updated from:287a78c1e1. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING200
linux-devel-x86_64NOTE448
source / vignettesOK322
linux-release-x86_64NOTE373
macos-release-arm64NOTE234
macos-oldrel-arm64NOTE224
windows-develNOTE421
windows-releaseNOTE495
windows-oldrelNOTE505
wasm-releaseOK181

Exports:preprocessresultsscDDsideViolinsimulateSettestKS

Dependencies:abindarmassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblockmodelingblusterbootbriocallrcaToolscliclustercodacodetoolscpp11crayonDelayedArraydescdiffobjdotCall64dqrngEBSeqedgeRevaluatefarverfieldsformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegplotsgtablegtoolsigraphIRangesirlbaisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmetapodminqanlmenloptroutlierspkgbuildpkgconfigpkgloadpraiseprocessxpsR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrprojrootrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscranscuttleSeqinfoSingleCellExperimentsitmosnowspamSparseArraystatmodSummarizedExperimenttestthatvctrsviridisLitewaldowithrXVector

scDD Quickstart

Rendered fromscDD.Rnwusingknitr::knitron May 30 2026.

Last update: 2018-03-23
Started: 2016-12-14

Readme and manuals

Help Manual

Help pageTopics
calcMVcalcMV
calcRPcalcRP
classifyDDclassifyDD
feDPfeDP
findFCfindFC
findIndexfindIndex
findOutliersfindOutliers
getPosteriorParamsgetPosteriorParams
jointPosteriorjointPosterior
lulu
luOutlierluOutlier
mclustRestrictedmclustRestricted
permMclustpermMclust
permMclustCovpermMclustCov
permMclustGenepermMclustGene
permZeropermZero
preprocesspreprocess
resultsresults
Data: Toy example datascDatEx
Data: Toy example data listscDatExList
Data: Toy example of simulated datascDatExSim
scDDscDD
sideHistsideHist
sideViolinsideViolin
simuDBsimuDB
simuDEsimuDE
simuDMsimuDM
simuDPsimuDP
simulateSetsimulateSet
singleCellSimusingleCellSimu
testKStestKS
testZeroestestZeroes
validationvalidation