Package: MMDiff2 1.40.0

Gabriele Schweikert

MMDiff2: Statistical Testing for ChIP-Seq data sets

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

Authors:Gabriele Schweikert [cre, aut], David Kuo [aut]

MMDiff2_1.40.0.tar.gz
MMDiff2_1.40.0.zip(r-4.7)MMDiff2_1.40.0.zip(r-4.6)MMDiff2_1.40.0.zip(r-4.5)
MMDiff2_1.40.0.tgz(r-4.6-any)MMDiff2_1.40.0.tgz(r-4.5-any)
MMDiff2_1.40.0.tar.gz(r-4.7-any)MMDiff2_1.40.0.tar.gz(r-4.6-any)
MMDiff2_1.40.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MMDiff2/json (API)

# Install 'MMDiff2' in R:
install.packages('MMDiff2', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • MMD - DBAmmd Object for Cfp1 example

On BioConductor:MMDiff2-1.41.0(bioc 3.24)MMDiff2-1.40.0(bioc 3.23)

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

chipseqdifferentialpeakcallingsequencingsoftware

3.48 score 3 scripts 392 downloads 24 exports 87 dependencies

Last updated from:6c8c790bb3 (on RELEASE_3_23). Checks:4 WARNING, 4 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING270
linux-devel-x86_64NOTE530
source / vignettesOK402
linux-release-x86_64NOTE543
macos-release-arm64NOTE386
macos-oldrel-arm64NOTE292
windows-develWARNING420
windows-releaseWARNING370
windows-oldrelWARNING367
wasm-releaseOK223

Exports:compDistscompHistscompPvalsContrastCountsDBAmmdDistsestimateFragmentCentersGenomegetPeakReadsHistsmetaDatanumPeaksnumSamplesplotDistsplotDISTS4PeakplotPeakReadsRegionsreportResultsrunShinyMMDiff2SamplessetContrastsetRegions

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemcigarilloclicodetoolscommonmarkcpp11crayoncurlDelayedArraydigestfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehtmltoolshttpuvhttrIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclelocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshinysnowsourcetoolsSparseArraySummarizedExperimentsysvctrsviridisLitewithrXMLxtableXVectoryaml

An Introduction to the MMDiff2 method

Rendered fromMMDiff2.Rnwusingknitr::knitron May 29 2026.

Last update: 2016-04-26
Started: 2016-04-25

Readme and manuals

Help Manual

Help pageTopics
Peaks for Cfp1-data setCfp1-Peaks
Compute distances between PeakscompDists
Compute Peak histogramscompHists
compute p-valuescompPvals
Extract data from DBAmmd objectsContrast,DBAmmd-method Counts,DBAmmd-method DBAmmd-Accessors Dists,DBAmmd-method Genome,DBAmmd-method Hists,DBAmmd-method metaData,DBAmmd-method numPeaks,DBAmmd-method numSamples,DBAmmd-method Reads,DBAmmd-method Regions,DBAmmd-method Samples,DBAmmd-method setContrast,DBAmmd-method setRegions,DBAmmd-method
Class DBAmmdDBAmmd DBAmmd-class
estimate center of fragmentsestimateFragmentCenters
Get reads from indexed bam files for defined regionsgetPeakReads
Generics for DBAmmd-ClassContrast Counts Dists Genome Hists metaData numPeaks numSamples Reads Regions Samples setContrast setRegions
mm9-Genesmm9-Genes
DBAmmd Object for Cfp1 exampleMMD
plotDistsplotDists
plotDISTS4PeakplotDISTS4Peak
plot PeakplotPeak
report resultsreportResults
Shiny Application for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaksrunShinyMMDiff2
Shiny server code for interactive visualization of MMD distances, peak plots, and MMD distances by sample.server.MMDiff2
ui component for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaksui.MMDiff2