Quickstart | Inputs | Options | Background nucleotide frequencies | Log base and pseudocounts | P value | Outputs | Session Info
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:
motifmatchr_1.35.0.tar.gz
motifmatchr_1.35.0.zip(r-4.7)motifmatchr_1.35.0.zip(r-4.6)motifmatchr_1.33.0.zip(r-4.5)
motifmatchr_1.35.0.tgz(r-4.6-x86_64)motifmatchr_1.35.0.tgz(r-4.6-arm64)motifmatchr_1.33.0.tgz(r-4.5-x86_64)motifmatchr_1.33.0.tgz(r-4.5-arm64)
motifmatchr_1.35.0.tar.gz(r-4.7-arm64)motifmatchr_1.35.0.tar.gz(r-4.7-x86_64)motifmatchr_1.35.0.tar.gz(r-4.6-arm64)motifmatchr_1.35.0.tar.gz(r-4.6-x86_64)
motifmatchr_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
motifmatchr/json (API)
| # Install 'motifmatchr' in R: |
| install.packages('motifmatchr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- example_motifs - Example_motifs
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.
Last updated from:0aa3d5188f. Checks:1 WARNING, 8 NOTE, 2 OK, 3 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 260 | ||
| linux-devel-arm64 | NOTE | 415 | ||
| linux-devel-x86_64 | NOTE | 487 | ||
| source / vignettes | OK | 418 | ||
| linux-release-arm64 | NOTE | 361 | ||
| linux-release-x86_64 | NOTE | 467 | ||
| macos-release-arm64 | NOTE | 393 | ||
| macos-release-x86_64 | NOTE | 487 | ||
| macos-oldrel-arm64 | FAIL | 133 | ||
| macos-oldrel-x86_64 | FAIL | 310 | ||
| windows-devel | NOTE | 398 | ||
| windows-release | NOTE | 386 | ||
| windows-oldrel | FAIL | 160 | ||
| wasm-release | OK | 541 |
Exports:match_motifsmatchMotifsmotif_countsmotif_matchesmotif_scoresmotifCountsmotifMatchesmotifScorespwmType
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayDirichletMultinomialfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrIRangesjsonlitelambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpwalignR6RcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraySummarizedExperimentsysTFBSToolsTFMPvaluevctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| example_motifs | example_motifs |
| matchMotifs | matchMotifs 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 |
| motifCounts | motifCounts motifCounts,SummarizedExperiment-method |
| motifMatches | motifMatches motifMatches,SummarizedExperiment-method |
| motifmatchr: Fast Motif Matching in R | motifmatchr-package motifmatchr |
| Deprecated functions in motifmatchr | match_motifs motifmatchr_deprecated motif_counts motif_matches motif_scores |
| motifScores | motifScores motifScores,SummarizedExperiment-method |
