Package: motifcounter 1.29.0

Wolfgang Kopp

motifcounter: R package for analysing TFBSs in DNA sequences

'motifcounter' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.

Authors:Wolfgang Kopp [aut, cre]

motifcounter_1.29.0.tar.gz
motifcounter_1.29.0.zip(r-4.5)motifcounter_1.29.0.zip(r-4.4)motifcounter_1.29.0.zip(r-4.3)
motifcounter_1.29.0.tgz(r-4.4-arm64)motifcounter_1.29.0.tgz(r-4.4-x86_64)motifcounter_1.29.0.tgz(r-4.3-arm64)motifcounter_1.29.0.tgz(r-4.3-x86_64)
motifcounter_1.29.0.tar.gz(r-4.5-noble)motifcounter_1.29.0.tar.gz(r-4.4-noble)
motifcounter_1.29.0.tgz(r-4.4-emscripten)motifcounter_1.29.0.tgz(r-4.3-emscripten)
motifcounter.pdf |motifcounter.html✨
motifcounter/json (API)
NEWS

# Install 'motifcounter' in R:
install.packages('motifcounter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:motifcounter-1.29.0(bioc 3.20)motifcounter-1.28.0(bioc 3.19)

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

bioconductor-package

10 exports 1.24 score 18 dependencies 2 mentions

Last updated 2 months agofrom:a85abf54ca

Exports:motifcounterOptionsmotifEnrichmentmotifHitProfilemotifHitsnormalizeMotifreadBackgroundscoreDistscoreHistogramscoreProfilescoreSequence

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc

Introduction to the motifcounter package

Wolfgang Kopp

Rendered frommotifcounter.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2017-10-06
Started: 2016-11-25

Readme and manuals

Help Manual

Help pageTopics
TFBSs analysis in DNA sequencesmotifcounter-package motifcounter
Background class definition.Background Background-class
Clump size distributionclumpSizeDist
Combinatrial model approximation of the number of motif hitscombinatorialDist
Compound Poisson ApproximationcompoundPoissonDist
Computes the Clump start probability based on a Markov modelcomputeClumpStartProb
Generate DNAStringgenerateDNAString
Generate DNAStringSetgenerateDNAStringSet
Accessor to slot alphagetAlpha
Accessor to slot betagetBeta
Accessor to slot beta3pgetBeta3p
Accessor to slot betagetBeta5p
Accessor to slot countsgetCounts
Accessor to slot gammagetGamma
Accessor to slot ordergetOrder
Accessor to slot singlestrandedgetSinglestranded
Accessor to slot stationgetStation
Accessor to slot transgetTrans
Hit strandhitStrand
Length of sequences in a given fasta filelenSequences
Markov model for generating Y_1Y_2_Y3 ...markovModel
Check valididity of PFM with backgroundmotifAndBackgroundValid
Set parameters for the enrichment analysismotifcounterOptions
Enrichment of motif hitsmotifEnrichment
Motif hit profile across multiple sequencesmotifHitProfile
Motif hit observationsmotifHits
Check valididity of PFMmotifValid
Normalizes a PFMnormalizeMotif
Number of motif hits in a set of DNA sequencesnumMotifHits
Overlap class definition.Overlap Overlap-class
Overlapping motif hit probabilitiesprobOverlapHit
Estimates a background model from a set of DNA sequencesreadBackground
Reverse complements a PFMrevcompMotif
Score distributionscoreDist
Score distributionscoreDistBf
Empirical score distributionscoreDistEmpirical
Score histogramscoreHistogram
Score histogram on a single sequencescoreHistogramSingleSeq
Score profile across multiple sequencesscoreProfile
Score observationsscoreSequence
Score strandscoreStrand
Score thresholdscoreThreshold
Retrieve the false positive probabilitysigLevel
Empirical clump size distributionsimulateClumpSizeDist
Empirical number of motif hits distributionsimulateNumHitsDist