Package: motifmatchr 1.35.0

Alicia Schep

motifmatchr: Fast Motif Matching in R

Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.

Authors:Alicia Schep [aut, cre], Stanford University [cph]

motifmatchr_1.35.0.tar.gz
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motifmatchr_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
motifmatchr/json (API)
NEWS

# Install 'motifmatchr' in R:
install.packages('motifmatchr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:motifmatchr-1.35.0(bioc 3.24)motifmatchr-1.34.0(bioc 3.23)

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

motifannotationcpp

8.53 score 5 packages 1.0k scripts 2.9k downloads 5 mentions 9 exports 73 dependencies

Last updated from:0aa3d5188f. Checks:1 WARNING, 8 NOTE, 2 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING245
linux-devel-arm64NOTE413
linux-devel-x86_64NOTE662
source / vignettesOK410
linux-release-arm64NOTE382
linux-release-x86_64NOTE512
macos-release-arm64NOTE288
macos-release-x86_64NOTE827
macos-oldrel-arm64FAIL115
macos-oldrel-x86_64FAIL267
windows-develNOTE420
windows-releaseNOTE409
windows-oldrelFAIL174
wasm-releaseOK208

Exports:match_motifsmatchMotifsmotif_countsmotif_matchesmotif_scoresmotifCountsmotifMatchesmotifScorespwmType

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayDirichletMultinomialfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrIRangesjsonlitelambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpwalignR6RcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraySummarizedExperimentsysTFBSToolsTFMPvaluevctrsXMLXVectoryaml

motifmatchr

Rendered frommotifmatchr.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2017-05-18
Started: 2017-01-18

Readme and manuals

Help Manual

Help pageTopics
example_motifsexample_motifs
matchMotifsmatchMotifs matchMotifs,PFMatrix,ANY-method matchMotifs,PFMatrixList,ANY-method matchMotifs,PWMatrix,ANY-method matchMotifs,PWMatrixList,BSgenomeViews-method matchMotifs,PWMatrixList,character-method matchMotifs,PWMatrixList,DNAString-method matchMotifs,PWMatrixList,DNAStringSet-method matchMotifs,PWMatrixList,GenomicRanges-method matchMotifs,PWMatrixList,RangedSummarizedExperiment-method
motifCountsmotifCounts motifCounts,SummarizedExperiment-method
motifMatchesmotifMatches motifMatches,SummarizedExperiment-method
motifmatchr: Fast Motif Matching in Rmotifmatchr-package motifmatchr
Deprecated functions in motifmatchrmatch_motifs motifmatchr_deprecated motif_counts motif_matches motif_scores
motifScoresmotifScores motifScores,SummarizedExperiment-method