Package: MotifPeeker 1.4.0

Hiranyamaya Dash

MotifPeeker: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. Motif Discovery Enrichment Analysis) Statistics for the frequency of ab-initio discovered motifs enriched in the datasets and compared with known motifs.

Authors:Hiranyamaya Dash [cre, aut], Thomas Roberts [aut], Maria Weinert [aut], Nathan Skene [aut]

MotifPeeker_1.4.0.tar.gz
MotifPeeker_1.4.0.zip(r-4.7)MotifPeeker_1.4.0.zip(r-4.6)MotifPeeker_1.4.0.zip(r-4.5)
MotifPeeker_1.4.0.tgz(r-4.6-any)MotifPeeker_1.4.0.tgz(r-4.5-any)
MotifPeeker_1.4.0.tar.gz(r-4.7-any)MotifPeeker_1.4.0.tar.gz(r-4.6-any)
MotifPeeker_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MotifPeeker/json (API)
NEWS

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

Bug tracker:https://github.com/neurogenomics/motifpeeker/issues

Datasets:

On BioConductor:MotifPeeker-1.5.0(bioc 3.24)MotifPeeker-1.4.0(bioc 3.23)

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis

5.45 score 2 stars 7 scripts 197 downloads 20 exports 172 dependencies

Last updated from:35008efabb (on RELEASE_3_23). Checks:1 WARNING, 6 OK, 3 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING365
linux-devel-x86_64OK666
source / vignettesOK552
linux-release-x86_64OK608
macos-release-arm64OK326
macos-oldrel-arm64OK313
windows-develERROR572
windows-releaseERROR531
windows-oldrelERROR636
wasm-releaseOK383

Exports:%>%bootstrap_distancescalc_fripcheck_ENCODEcheck_genome_buildcheck_JASPARdenovo_motifsfind_motifsget_df_distancesget_df_distances_bootstrappedget_df_enrichmentget_JASPARCOREmotif_enrichmentmotif_similarityMotifPeekerread_motif_fileread_peak_filesave_peak_filesegregate_seqssummit_to_motif

Dependencies:abindaskpassassertthatbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbrioBSgenomebslibcacachemcallrcigarilloclicliprclustercmdfuncodetoolscolorspacecpp11crayoncredentialscrosstalkcurldata.tableDBIdbplyrDelayedArraydendextenddescdiffobjdigestdplyrDTeggevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomicAlignmentsGenomicRangesgertggplot2gitcredsgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2iniIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemesmemoisemgcvmimenlmeopensslotelpatchworkpermutepillarpkgbuildpkgconfigpkgloadplotlyplyrpraiseprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppThreadRCurlreadrregistryreshape2restfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseriationsnowSparseArraystringistringrSummarizedExperimentsystestthattibbletidyrtidyselecttinytexTSPtzdbuniversalmotifusethisutf8vctrsveganviridisviridisLitevroomwaldowebshotwhiskerwithrxfunXMLxml2XVectoryamlzip

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Rendered fromMotifPeeker.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2025-11-20
Started: 2024-07-10

Troubleshooting

Rendered fromtroubleshooting.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2024-11-12
Started: 2024-07-11