{ "_id": "6a1fdaeeb401979e73437a57", "Package": "motifcounter", "Type": "Package", "Title": "R package for analysing TFBSs in DNA sequences", "Version": "1.36.0", "Date": "2017", "Author": "Wolfgang Kopp [aut, cre]", "Maintainer": "Wolfgang Kopp ", "Description": "'motifcounter' provides motif matching, motif counting and\nmotif enrichment functionality based on position frequency\nmatrices. The main features of the packages include the\nutilization of higher-order background models and accounting\nfor self-overlapping motif matches when determining motif\nenrichment. The background model allows to capture dinucleotide\n(or higher-order nucleotide) composition adequately which may\nreduced model biases and misleading results compared to using\nsimple GC background models. When conducting a motif enrichment\nanalysis based on the motif match count, the package relies on\na compound Poisson distribution or alternatively a\ncombinatorial model. These distribution account for\nself-overlapping motif structures as exemplified by repeat-like\nor palindromic motifs, and allow to determine the p-value and\nfold-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'\n'combinatorial_wrapper.R' 'score_wrapper.R' 'count_wrapper.R'\n'enrichmentTest.R' 'forground_wrapper.R' 'markovmodel.R'\n'motifcounter-package.R' 'observed_wrapper.R' 'option.R'\n'overlap.R' 'simulate_wrapper.R' 'wrapper.R' 'zzz.R'", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:45:19 UTC", "RemoteUrl": "https://github.com/bioc/motifcounter", "RemoteRef": "RELEASE_3_23", "RemoteSha": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "Packaged": { "Date": "2026-06-03 07:30:56 UTC", "User": "root" }, "MD5sum": "20080ee2159696c012a44c47d9cfa87a", "_user": "bioc-release", "_type": "src", "_file": "motifcounter_1.36.0.tar.gz", "_fileid": "17eef78b2fa8c935c71d4ed3b2e4c1f2081eff0188f662134c700b83f5d8e113", "_filesize": 964945, "_sha256": "17eef78b2fa8c935c71d4ed3b2e4c1f2081eff0188f662134c700b83f5d8e113", "_created": "2026-06-03T07:30:56.000Z", "_published": "2026-06-03T07:42:38.511Z", "_jobs": [ { "job": 79243836948, "time": 164, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7378364687" }, { "job": 79243837022, "time": 266, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7378397564" }, { "job": 79243837030, "time": 367, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7378428913" }, { "job": 79243837025, "time": 271, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7378399539" }, { "job": 79243836994, "time": 313, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7378411312" }, { "job": 79243837011, "time": 152, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7378426558" }, { "job": 79243837006, "time": 452, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7378521293" }, { "job": 79243836977, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7378419586" }, { "job": 79243837012, "time": 432, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7378516604" }, { "job": 79243239195, "time": 239, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7378312861" }, { "job": 79243836990, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7378358277" }, { "job": 79243837005, "time": 368, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7378429302" }, { "job": 79243837262, "time": 367, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7378429187" }, { "job": 79243836991, "time": 361, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7378427160" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/motifcounter", "_commit": { "id": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380319 }, "_maintainer": { "name": "Wolfgang Kopp", "email": "wolfgang.kopp@mdc-berlin.de", "login": "wkopp", "description": "\n Researcher at the BIMSB - Max Delbrück center for molecular medicine.\n", "uuid": 3275747 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "MotifDb", "role": "Suggests" }, { "package": "seqLogo", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-06", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "transcription", "motifannotation", "sequencematching", "software", "openmp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 331, "source": "https://www.bioconductor.org/packages/stats/bioc/motifcounter" }, "_mentions": 2, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/motifcounter.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "motifcounterOptions", "motifEnrichment", "motifHitProfile", "motifHits", "normalizeMotif", "readBackground", "scoreDist", "scoreHistogram", "scoreProfile", "scoreSequence" ], "_help": [ { "page": "motifcounter-package", "title": "TFBSs analysis in DNA sequences", "topics": [ "motifcounter-package", "motifcounter" ] }, { "page": "Background-class", "title": "Background class definition", "topics": [ ".Background", "Background-class" ] }, { "page": "clumpSizeDist", "title": "Clump size distribution", "topics": [ "clumpSizeDist" ] }, { "page": "combinatorialDist", "title": "Combinatrial model approximation of the number of motif hits", "topics": [ "combinatorialDist" ] }, { "page": "compoundPoissonDist", "title": "Compound Poisson Approximation", "topics": [ "compoundPoissonDist" ] }, { "page": "computeClumpStartProb", "title": "Computes the Clump start probability based on a Markov model", "topics": [ "computeClumpStartProb" ] }, { "page": "generateDNAString", "title": "Generate DNAString", "topics": [ "generateDNAString" ] }, { "page": "generateDNAStringSet", "title": "Generate DNAStringSet", "topics": [ "generateDNAStringSet" ] }, { "page": "getAlpha", "title": "Accessor to slot alpha", "topics": [ "getAlpha" ] }, { "page": "getBeta", "title": "Accessor to slot beta", "topics": [ "getBeta" ] }, { "page": "getBeta3p", "title": "Accessor to slot beta3p", "topics": [ "getBeta3p" ] }, { "page": "getBeta5p", "title": "Accessor to slot beta", "topics": [ "getBeta5p" ] }, { "page": "getCounts", "title": "Accessor to slot counts", "topics": [ "getCounts" ] }, { "page": "getGamma", "title": "Accessor to slot gamma", "topics": [ "getGamma" ] }, { "page": "getOrder", "title": "Accessor to slot order", "topics": [ "getOrder" ] }, { "page": "getSinglestranded", "title": "Accessor to slot singlestranded", "topics": [ "getSinglestranded" ] }, { "page": "getStation", "title": "Accessor to slot station", "topics": [ "getStation" ] }, { "page": "getTrans", "title": "Accessor to slot trans", "topics": [ "getTrans" ] }, { "page": "hitStrand", "title": "Hit strand", "topics": [ "hitStrand" ] }, { "page": "lenSequences", "title": "Length of sequences in a given fasta file", "topics": [ "lenSequences" ] }, { "page": "markovModel", "title": "Markov model for generating Y_1Y_2_Y3 ...", "topics": [ "markovModel" ] }, { "page": "motifAndBackgroundValid", "title": "Check valididity of PFM with background", "topics": [ "motifAndBackgroundValid" ] }, { "page": "motifcounterOptions", "title": "Set parameters for the enrichment analysis", "topics": [ "motifcounterOptions" ] }, { "page": "motifEnrichment", "title": "Enrichment of motif hits", "topics": [ "motifEnrichment" ] }, { "page": "motifHitProfile", "title": "Motif hit profile across multiple sequences", "topics": [ "motifHitProfile" ] }, { "page": "motifHits", "title": "Motif hit observations", "topics": [ "motifHits" ] }, { "page": "motifValid", "title": "Check valididity of PFM", "topics": [ "motifValid" ] }, { "page": "normalizeMotif", "title": "Normalizes a PFM", "topics": [ "normalizeMotif" ] }, { "page": "numMotifHits", "title": "Number of motif hits in a set of DNA sequences", "topics": [ "numMotifHits" ] }, { "page": "Overlap-class", "title": "Overlap class definition", "topics": [ ".Overlap", "Overlap-class" ] }, { "page": "probOverlapHit", "title": "Overlapping motif hit probabilities", "topics": [ "probOverlapHit" ] }, { "page": "readBackground", "title": "Estimates a background model from a set of DNA sequences", "topics": [ "readBackground" ] }, { "page": "revcompMotif", "title": "Reverse complements a PFM", "topics": [ "revcompMotif" ] }, { "page": "scoreDist", "title": "Score distribution", "topics": [ "scoreDist" ] }, { "page": "scoreDistBf", "title": "Score distribution", "topics": [ "scoreDistBf" ] }, { "page": "scoreDistEmpirical", "title": "Empirical score distribution", "topics": [ "scoreDistEmpirical" ] }, { "page": "scoreHistogram", "title": "Score histogram", "topics": [ "scoreHistogram" ] }, { "page": "scoreHistogramSingleSeq", "title": "Score histogram on a single sequence", "topics": [ "scoreHistogramSingleSeq" ] }, { "page": "scoreProfile", "title": "Score profile across multiple sequences", "topics": [ "scoreProfile" ] }, { "page": "scoreSequence", "title": "Score observations", "topics": [ "scoreSequence" ] }, { "page": "scoreStrand", "title": "Score strand", "topics": [ "scoreStrand" ] }, { "page": "scoreThreshold", "title": "Score threshold", "topics": [ "scoreThreshold" ] }, { "page": "sigLevel", "title": "Retrieve the false positive probability", "topics": [ "sigLevel" ] }, { "page": "simulateClumpSizeDist", "title": "Empirical clump size distribution", "topics": [ "simulateClumpSizeDist" ] }, { "page": "simulateNumHitsDist", "title": "Empirical number of motif hits distribution", "topics": [ "simulateNumHitsDist" ] } ], "_readme": "https://github.com/bioc/motifcounter/raw/RELEASE_3_23/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_sysdeps": [ { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "motifcounter.Rmd", "filename": "motifcounter.html", "title": "Introduction to the motifcounter package", "author": "Wolfgang Kopp", "engine": "knitr::rmarkdown", "headings": [ "Usage examples", "Introduction", "Biological background", "Hallmarks of motifcounter", "Getting started", "Preliminary steps", "Acquire a background model", "Optional settings", "Retrieve position- and strand-specific scores and hits", "Analysis of individual DNA sequences", "Analysis of a set of DNA sequences", "Test for motif hit enrichment", "Session Info" ], "created": "2016-11-25 10:34:52", "modified": "2017-10-06 19:08:13", "commits": 20 } ], "_score": 3.518513939877888, "_indexed": false, "_nocasepkg": "motifcounter", "_universes": [ "bioc-release" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.36.0", "date": "2026-06-03T07:33:54.000Z", "distro": "noble", "arch": "aarch64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "8df36ff4f9c50f968ca09482e33982c66fa82d6b259bda7865083cf7897d21ef", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.7.0", "os": "linux", "version": "1.36.0", "date": "2026-06-03T07:35:31.000Z", "distro": "noble", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "3dda7e6c6e33821ee3205e194197fda21a5322bb09176b4a07e9afff20471966", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "linux", "version": "1.36.0", "date": "2026-06-03T07:34:00.000Z", "distro": "noble", "arch": "aarch64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "7f0e28a160144004f89ef0dbaf7a8b2bb29ea5239bfde50fd6612b41e91661a7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "linux", "version": "1.36.0", "date": "2026-06-03T07:34:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "f9412ba964764e1eec381db1850bf6cfc26934d5f4a115de1ed503f40b1da60d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.5.3", "os": "mac", "version": "1.36.0", "date": "2026-06-03T07:36:01.000Z", "arch": "aarch64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "e74c964e978a3d78d500cd101e969233ffc5f997a086073586b8da8c4cc54122", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.5.3", "os": "mac", "version": "1.36.0", "date": "2026-06-03T07:38:38.000Z", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "cd99f7ba6aac1a2842db8ea11c04535707e145ce26d2e75d0229299838e16a3b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "mac", "version": "1.36.0", "date": "2026-06-03T07:35:48.000Z", "arch": "aarch64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "e132c220395dc15e70175aca959a31376dba194e1d3dbe5721155860ffeec07c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "mac", "version": "1.36.0", "date": "2026-06-03T07:37:53.000Z", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "086d84d2bc5a227399daf9c7604f25bef9137fa185b47cc3c3a30800d5aa96ae", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "wasm", "version": "1.36.0", "date": "2026-06-03T07:33:40.000Z", "arch": "emscripten", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "5af2da98d9e70850427183f2862a3e71812522ae2ab5428860ba829473aaa889", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.7.0", "os": "win", "version": "1.36.0", "date": "2026-06-03T07:33:02.000Z", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "e76a279a392ce7000b3d6801cf8eaac3189c0be63ca768bfea472379d56b9fb2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.5.3", "os": "win", "version": "1.36.0", "date": "2026-06-03T07:32:38.000Z", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "66912c9b96ad08df58ba5364f5d6cbd1eba3712e38d2dd6c19b824d137f48834", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" }, { "r": "4.6.0", "os": "win", "version": "1.36.0", "date": "2026-06-03T07:32:47.000Z", "arch": "x86_64", "commit": "d547964fad9c9e88c391f7fb79173f7a3e8d0718", "fileid": "1db8fcf3d9465a1fed7f15d5cb889de02eeda672b1432f8d77f66a3cef24c57f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26870148994" } ] }