Package: motifcounter
Type: Package
Title: R package for analysing TFBSs in DNA sequences
Version: 1.36.0
Date: 2017
Author: Wolfgang Kopp [aut, cre]
Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
Imports: Biostrings, methods
Depends: R(>= 3.0)
Maintainer: Wolfgang Kopp <wolfgang.kopp@mdc-berlin.de>
Description: '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.
License: GPL-2
biocViews: Transcription,MotifAnnotation,SequenceMatching,Software
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Collate: 'background_wrapper.R' 'comppoiss_wrapper.R'
        'combinatorial_wrapper.R' 'score_wrapper.R' 'count_wrapper.R'
        'enrichmentTest.R' 'forground_wrapper.R' 'markovmodel.R'
        'motifcounter-package.R' 'observed_wrapper.R' 'option.R'
        'overlap.R' 'simulate_wrapper.R' 'wrapper.R' 'zzz.R'
PackageStatus: Deprecated
Config/pak/sysreqs: zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:45:19 UTC
RemoteUrl: https://github.com/bioc/motifcounter
RemoteRef: RELEASE_3_23
RemoteSha: d547964fad9c9e88c391f7fb79173f7a3e8d0718
Packaged: 2026-07-25 06:54:13 UTC; root