Package: MotifPeeker 0.99.13

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. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo 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_0.99.13.tar.gz
MotifPeeker_0.99.13.zip(r-4.5)MotifPeeker_0.99.13.zip(r-4.4)
MotifPeeker_0.99.13.tgz(r-4.5-any)MotifPeeker_0.99.13.tgz(r-4.4-any)
MotifPeeker_0.99.13.tar.gz(r-4.5-noble)MotifPeeker_0.99.13.tar.gz(r-4.4-noble)
MotifPeeker_0.99.13.tgz(r-4.4-emscripten)
MotifPeeker.pdf |MotifPeeker.html
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-0.99.13(bioc 3.21)

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis

5.48 score 2 stars 6 scripts 38 downloads 18 exports 177 dependencies

Last updated 2 months agofrom:665ef162ae. Checks:3 OK, 2 NOTE, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 08 2025
R-4.5-winERRORMar 08 2025
R-4.5-macNOTEMar 08 2025
R-4.5-linuxNOTEMar 08 2025
R-4.4-winERRORMar 08 2025
R-4.4-macOKMar 08 2025
R-4.4-linuxOKMar 08 2025

Exports:%>%calc_fripcheck_ENCODEcheck_genome_buildcheck_JASPARdenovo_motifsfind_motifsget_df_distancesget_df_enrichmentget_JASPARCOREmotif_enrichmentmotif_similarityMotifPeekerread_motif_fileread_peak_filesave_peak_filesegregate_seqssummit_to_motif

Dependencies:abindaskpassassertthatbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbrioBSgenomebslibcacachemcallrclicliprclustercmdfuncodetoolscolorspacecpp11crayoncredentialscrosstalkcurldata.tableDBIdbplyrDelayedArraydendextenddescdiffobjdigestdplyrDTeggevaluatefansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgertggplot2ggseqlogoghgitcredsgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2iniIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemesmemoisemgcvmimemunsellnlmeopensslpatchworkpermutepillarpkgbuildpkgconfigpkgloadplogrplotlyplyrpraiseprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppThreadRCurlreadrregistryreshape2restfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesseriationsnowSparseArraystringistringrSummarizedExperimentsystestthattibbletidyrtidyselecttinytexTSPtzdbUCSC.utilsuniversalmotifusethisutf8vctrsveganviridisviridisLitevroomwaldowebshotwhiskerwithrxfunXMLxml2XVectoryamlzip

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Last update: 2024-12-02
Started: 2024-07-10

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