Package: motifmatchr 1.29.0

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]

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motifmatchr.pdf |motifmatchr.html✨
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:

example_motifs - Example_motifs

On BioConductor:motifmatchr-1.29.0(bioc 3.21)motifmatchr-1.28.0(bioc 3.20)

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

motifannotation cpp

8.12 score 5 packages 722 scripts 2.5k downloads 5 mentions 9 exports 117 dependencies

Last updated 4 months agofrom:0c153099eb. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 17 2025
R-4.5-win-x86_64	NOTE	Feb 17 2025
R-4.5-linux-x86_64	NOTE	Feb 17 2025
R-4.4-win-x86_64	NOTE	Feb 17 2025
R-4.4-mac-x86_64	NOTE	Feb 17 2025
R-4.4-mac-aarch64	NOTE	Feb 17 2025
R-4.3-win-x86_64	NOTE	Feb 17 2025
R-4.3-mac-x86_64	NOTE	Feb 17 2025
R-4.3-mac-aarch64	NOTE	Feb 17 2025

Exports:match_motifs matchMotifs motif_counts motif_matches motif_scores motifCounts motifMatches motifScores pwmType

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cli clipr CNEr codetools colorspace cpp11 crayon curl DBI DelayedArray DirichletMultinomial fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales seqLogo snow SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xtable XVector yaml

motifmatchr

Rendered frommotifmatchr.Rmdusingknitr::rmarkdownon Feb 17 2025.

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

Citation

Development and contributors

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