Package: MotifPeeker 1.5.0

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_1.5.0.tar.gz
MotifPeeker_1.5.0.zip(r-4.7)MotifPeeker_1.5.0.zip(r-4.6)MotifPeeker_1.5.0.zip(r-4.5)
MotifPeeker_1.5.0.tgz(r-4.6-any)MotifPeeker_1.5.0.tgz(r-4.5-any)
MotifPeeker_1.5.0.tar.gz(r-4.7-any)MotifPeeker_1.5.0.tar.gz(r-4.6-any)
MotifPeeker_1.5.0.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.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

5.51 score 2 stars 7 scripts 228 downloads 20 exports 173 dependencies

Last updated from:09c90284ea. Checks:1 WARNING, 6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING444
linux-devel-x86_64OK568
source / vignettesOK422
linux-release-x86_64OK595
macos-release-arm64OK450
macos-oldrel-arm64OK454
windows-develERROR518
windows-releaseERROR762
windows-oldrelERROR491
wasm-releaseOK401

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:abindaskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbrioBSgenomebslibcacachemcallrcigarilloclicliprclustercmdfuncodetoolscolorspacecpp11crayoncredentialscrosstalkcurldata.tableDBIdbplyrDelayedArraydendextenddescdiffobjdigestdplyrDTeggevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomicAlignmentsGenomicRangesgertggplot2gitcredsgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2iniIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemesmemoisemgcvmimenlmeopensslotelpatchworkpermutepillarpkgbuildpkgconfigpkgloadplotlyplyrpraiseprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppThreadRCurlreadrregistryreshape2restfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseriationsnowSparseArraystringistringrSummarizedExperimentsystestthattibbletidyrtidyselecttinytexTSPtzdbuniversalmotifusethisutf8vctrsveganviridisviridisLitevroomwaldowebshotwhiskerwithrxfunXMLxml2XVectoryamlzip

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Rendered fromMotifPeeker.Rmdusingknitr::rmarkdownon May 30 2026.

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

Troubleshooting

Rendered fromtroubleshooting.Rmdusingknitr::rmarkdownon May 30 2026.

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