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:
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-4.4-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
- CTCF_ChIP_peaks - Example ChIP-seq peak file
- CTCF_TIP_peaks - Example TIP-seq peak file
- motif_MA1102.3 - Example CTCFL JASPAR motif file
- motif_MA1930.2 - Example CTCF JASPAR motif file
On BioConductor:MotifPeeker-0.99.12(bioc 3.21)
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis
Last updated 10 days agofrom:45eb2ac271. Checks:OK: 2 NOTE: 1 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 20 2024 |
| R-4.5-win | ERROR | Dec 20 2024 |
| R-4.5-linux | NOTE | Dec 20 2024 |
| R-4.4-win | ERROR | Dec 20 2024 |
| R-4.4-mac | OK | Dec 20 2024 |
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.utilsuniversalmotifusethisutf8vctrsveganviridisviridisLitevroomwaldowebshotwhiskerwithrxfunXMLxml2XVectoryamlzipzlibbioc
