Package: MMDiff2 1.35.0

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_1.35.0.tar.gz
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MMDiff2.pdf |MMDiff2.html✨
MMDiff2/json (API)

# Install 'MMDiff2' in R:
install.packages('MMDiff2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • MMD - DBAmmd Object for Cfp1 example

On BioConductor:MMDiff2-1.35.0(bioc 3.21)MMDiff2-1.34.0(bioc 3.20)

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

chipseqdifferentialpeakcallingsequencingsoftware

3.30 score 194 downloads 24 exports 97 dependencies

Last updated 2 months agofrom:d7fad9d06a. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winWARNINGDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winWARNINGDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winWARNINGDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:compDistscompHistscompPvalsContrastCountsDBAmmdDistsestimateFragmentCentersGenomegetPeakReadsHistsmetaDatanumPeaksnumSamplesplotDistsplotDISTS4PeakplotPeakReadsRegionsreportResultsrunShinyMMDiff2SamplessetContrastsetRegions

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemclicodetoolscolorspacecommonmarkcpp11crayoncurlDelayedArraydigestfansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehtmltoolshttpuvhttrIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigpromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssassscalesshinysnowsourcetoolsSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioc

An Introduction to the MMDiff2 method

Rendered fromMMDiff2.Rnwusingknitr::knitron Dec 19 2024.

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