{ "_id": "6a1aaeca1d7bb097a09d4efb", "Package": "PWMEnrich", "Type": "Package", "Title": "PWM enrichment analysis", "Version": "4.49.0", "Date": "2015-09-25", "Author": "Robert Stojnic, Diego Diez", "Maintainer": "Diego Diez ", "LazyLoad": "yes", "Description": "A toolkit of high-level functions for DNA motif scanning\nand enrichment analysis built upon Biostrings. The main\nfunctionality is PWM enrichment analysis of already known PWMs\n(e.g. from databases such as MotifDb), but the package also\nimplements high-level functions for PWM scanning and\nvisualisation. The package does not perform \"de novo\" motif\ndiscovery, but is instead focused on using motifs that are\neither experimentally derived or computationally constructed by\nother tools.", "License": "LGPL (>= 2)", "biocViews": "MotifAnnotation, SequenceMatching, Software", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:37 UTC", "RemoteUrl": "https://github.com/bioc/PWMEnrich", "RemoteRef": "HEAD", "RemoteSha": "4526a80ece5f118df1b2bc462f9c919d5671bbd9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:02:42 UTC", "User": "root" }, "MD5sum": "0011a11c67a275b251b7a79ea359db98", "_user": "bioc", "_type": "src", "_file": "PWMEnrich_4.49.0.tar.gz", "_fileid": "be4d58fa557189f3ead10346c29623869d64487d2e4280249a63f65c0c3c3b73", "_filesize": 1889800, "_sha256": "be4d58fa557189f3ead10346c29623869d64487d2e4280249a63f65c0c3c3b73", 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"_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "grid", "role": "Imports" }, { "package": "seqLogo", "role": "Imports" }, { "package": "gdata", "role": "Imports" }, { "package": "evd", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "MotifDb", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" }, { "package": "BSgenome.Dmelanogaster.UCSC.dm3", "role": "Suggests" }, { "package": "PWMEnrich.Dmelanogaster.background", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "gtools", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "PWMEnrich.Hsapiens.background", "role": "Suggests" }, { "package": "PWMEnrich.Mmusculus.background", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "4.49.0", "bioc": "3.24" }, { "branch": "release", "version": "4.48.0", "bioc": "3.23" } ], "_topics": [ "motifannotation", "sequencematching", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 565, "source": "https://www.bioconductor.org/packages/stats/bioc/PWMEnrich" }, "_mentions": 16, "_searchresults": 95, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PWMEnrich.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "as.data.frame", "getBackgroundFrequencies", "groupReport", "makeBackground", "makePriors", "makePWMCutoffBackground", "makePWMEmpiricalBackground", "makePWMGEVBackground", "makePWMLognBackground", "makePWMPvalCutoffBackground", "makePWMPvalCutoffBackgroundFromSeq", "motifDiffEnrichment", "motifEcdf", "motifEnrichment", "motifIC", "motifRankingForGroup", "motifRankingForSequence", "motifScores", "motifSimilarity", "PFMtoPWM", "plot", "plotMotifScores", "plotMultipleMotifs", "plotTopMotifsGroup", "plotTopMotifsSequence", "PWMUnscaled", "readMotifs", "registerCoresPWMEnrich", "reverseComplement", "scanWithPWM", "seqLogoGrid", "sequenceReport", "toPWM", "useBigMemoryPWMEnrich" ], "_help": [ { "page": "dot-inputParamMotifs", "title": "Normalizes the motifs input argument for multiple functions", "topics": [ ".inputParamMotifs" ] }, { "page": "dot-inputParamSequences", "title": "Normalize the sequences input argument", "topics": [ ".inputParamSequences" ] }, { "page": "dot-inputPFMfromMatrixOrPWM", "title": "Check the frequency matrix input parameter for motifSimilarity", "topics": [ ".inputPFMfromMatrixOrPWM" ] }, { "page": "dot-normalize.bg.seq", "title": "check consistency of bg.seq input parameter", "topics": [ ".normalize.bg.seq" ] }, { "page": "dot-normargPfm", "title": "Input parameter normalization for PWMUnscaled", "topics": [ ".normargPfm" ] }, { "page": "dot-normargPriorParams", "title": "Input parameter normalization function for PWMUnscaled", "topics": [ ".normargPriorParams" ] }, { "page": "subsetting-PWMCutoffBackground", "title": "Get the background for a subset of PWMs", "topics": [ "[,PWMCutoffBackground-method" ] }, { "page": "subsetting-PWMEmpiricalBackground", "title": "Get the background for a subset of PWMs", "topics": [ "[,PWMEmpiricalBackground-method" ] }, { "page": "subsetting-PWMGEVBackground", "title": "Get the background for a subset of PWMs", "topics": [ "[,PWMGEVBackground-method" ] }, { "page": "subsetting-PWMLognBackground", "title": "Get the background for a subset of PWMs", "topics": [ "[,PWMLognBackground-method" ] }, { "page": "affinitySequenceSet", "title": "Calculate total affinity over a set of sequences", "topics": [ "affinitySequenceSet" ] }, { "page": "as.data.frame-MotifEnrichmentReport-method", "title": "Convert a MotifEnrichmentReport into a data.frame object", "topics": [ "as.data.frame", "as.data.frame,MotifEnrichmentReport-method" ] }, { "page": "cloverPvalue1seq", "title": "Calculate the Clover P-value as described in the Clover paper", "topics": [ "cloverPvalue1seq" ] }, { "page": "cloverScore", "title": "Calculate the Clover score using the recursive formula from Frith et al", "topics": [ "cloverScore" ] }, { "page": "colMedians", "title": "Calculate medians of columns", "topics": [ "colMedians" ] }, { "page": "colSds", "title": "Calculate standard deviations of columns", "topics": [ "colSds" ] }, { "page": "concatenateSequences", "title": "Concatenata DNA sequences into a single character object", "topics": [ "concatenateSequences" ] }, { "page": "cutoffZscore", "title": "Z-score calculation for cutoff hits", "topics": [ "cutoffZscore" ] }, { "page": "cutoffZscoreSequenceSet", "title": "Z-score calculation for cutoff hits for group of sequences", "topics": [ "cutoffZscoreSequenceSet" ] }, { "page": "divideRows", "title": "Divide each row of a matrix with a vector", "topics": [ "divideRows" ] }, { "page": "DNAStringSetToList", "title": "Convert DNAStringSet to list of DNAString objects", "topics": [ "DNAStringSetToList" ] }, { "page": "empiricalPvalue", "title": "Calculate the empirical P-value by affinity of cutoff.", "topics": [ "empiricalPvalue" ] }, { "page": "empiricalPvalueSequenceSet", "title": "Empirical P-value for a set of sequences", "topics": [ "empiricalPvalueSequenceSet" ] }, { "page": "getBackgroundFrequencies", "title": "Get the four nucleotides background frequencies", "topics": [ "getBackgroundFrequencies" ] }, { "page": "getPromoters", "title": "Get the promoter sequences either for a named organism such as \"dm3\" or a BSgenome object", "topics": [ "getPromoters" ] }, { "page": "gevPerSequence", "title": "Apply GEV background normalization per every sequence", "topics": [ "gevPerSequence" ] }, { "page": "groupReport-MotifEnrichmentResults-method", "title": "Generate a motif enrichment report for the whole group of sequences together", "topics": [ "groupReport", "groupReport,MotifEnrichmentResults-method" ] }, { "page": "keepFinite", "title": "Replace all infinite values by 0", "topics": [ "keepFinite" ] }, { "page": "logNormPval", "title": "Calculate the P-value from lognormal distribution with background of equal length", "topics": [ "logNormPval" ] }, { "page": "logNormPvalSequenceSet", "title": "Lognormal P-value for a set of sequences", "topics": [ "logNormPvalSequenceSet" ] }, { "page": "makeBackground", "title": "Make a background for a set of position frequency matrices", "topics": [ "makeBackground" ] }, { "page": "makePriors", "title": "Make priors from background sequences", "topics": [ "makePriors" ] }, { "page": "makePWMCutoffBackground", "title": "Make a cutoff background", "topics": [ "makePWMCutoffBackground" ] }, { "page": "makePWMEmpiricalBackground", "title": "Make an empirical P-value background", "topics": [ "makePWMEmpiricalBackground" ] }, { "page": "makePWMGEVBackground", "title": "Make a GEV background distribution", "topics": [ "makePWMGEVBackground" ] }, { "page": "makePWMLognBackground", "title": "Make a lognormal background distribution", "topics": [ "makePWMLognBackground" ] }, { "page": "makePWMPvalCutoffBackground", "title": "Construct a cutoff background from empirical background", "topics": [ "makePWMPvalCutoffBackground" ] }, { "page": "makePWMPvalCutoffBackgroundFromSeq", "title": "Construct a P-value cutoff background from a set of sequences", "topics": [ "makePWMPvalCutoffBackgroundFromSeq" ] }, { "page": "makeStartEndPos", "title": "Divide total.len into fragments of length len by providing start,end positions", "topics": [ "makeStartEndPos" ] }, { "page": "matrixShuffleZscorePerSequence", "title": "Obtain z-score for motif column shuffling", "topics": [ "matrixShuffleZscorePerSequence" ] }, { "page": "maxAligned", "title": "Returned the aligned motif parts", "topics": [ "maxAligned" ] }, { "page": "motifDiffEnrichment", "title": "Differential motif enrichment", "topics": [ "motifDiffEnrichment" ] }, { "page": "motifEcdf", "title": "Calculate the empirical distribution score distribution for a set of motifs", "topics": [ "motifEcdf" ] }, { "page": "motifEnrichment", "title": "Motif enrichment", "topics": [ "motifEnrichment" ] }, { "page": "MotifEnrichmentReport-class", "title": "A report class with formatted results of motif enrichment", "topics": [ "MotifEnrichmentReport-class" ] }, { "page": "MotifEnrichmentResults-class", "title": "A wrapper class for results of motifEnrichment() that should make it easier to access the results.", "topics": [ "MotifEnrichmentResults-class" ] }, { "page": "motifIC", "title": "Information content for a PWM or PFM", "topics": [ "motifIC" ] }, { "page": "motifPrAUC", "title": "Calculate PR-AUC for motifs ranked according to some scoring scheme", "topics": [ "motifPrAUC" ] }, { "page": "motifRankingForGroup-MotifEnrichmentResults-method", "title": "Get a ranking of motifs by their enrichment in the whole set of sequences", "topics": [ "motifRankingForGroup", "motifRankingForGroup,MotifEnrichmentResults-method" ] }, { "page": "motifRankingForSequence-MotifEnrichmentResults-method", "title": "Get a ranking of motifs by their enrichment in one specific sequence", "topics": [ "motifRankingForSequence", "motifRankingForSequence,MotifEnrichmentResults-method" ] }, { "page": "motifRecoveryAUC", "title": "Calculate Recovery-AUC for motifs ranked according to some scoring scheme", "topics": [ "motifRecoveryAUC" ] }, { "page": "motifScores", "title": "Motif affinity or number of hits over a threshold", "topics": [ "motifScores" ] }, { "page": "motifScoresBigMemory", "title": "This is a memory intensive version of motifScore() which is about 2 times faster", "topics": [ "motifScoresBigMemory" ] }, { "page": "motifSimilarity", "title": "Calculates similarity between two PFMs.", "topics": [ "motifSimilarity" ] }, { "page": "operators-MotifEnrichmentReport", "title": "Names of variables", "topics": [ "$,MotifEnrichmentReport-method", "names,MotifEnrichmentReport", "names,MotifEnrichmentReport-method", "[,MotifEnrichmentReport-method" ] }, { "page": "operators-MotifEnrichmentResults", "title": "Names of variables", "topics": [ "$,MotifEnrichmentResults-method", "names,MotifEnrichmentResults", "names,MotifEnrichmentResults-method" ] }, { "page": "operators-PWM", "title": "Names of variables", "topics": [ "$,PWM-method", "length,PWM-method", "names,PWM", "names,PWM-method" ] }, { "page": "operators-PWMCutoffBackground", "title": "Names of variables", "topics": [ "$,PWMCutoffBackground-method", "names,PWMCutoffBackground", "names,PWMCutoffBackground-method" ] }, { "page": "operators-PWMEmpiricalBackground", "title": "Names of variables", "topics": [ "$,PWMEmpiricalBackground-method", "names,PWMEmpiricalBackground", "names,PWMEmpiricalBackground-method" ] }, { "page": "operators-PWMGEVBackground", "title": "Names of variables", "topics": [ "$,PWMGEVBackground-method", "names,PWMGEVBackground", "names,PWMGEVBackground-method" ] }, { "page": "operators-PWMLognBackground", "title": "Names of variables", "topics": [ "$,PWMLognBackground-method", "names,PWMLognBackground", "names,PWMLognBackground-method" ] }, { "page": "PFMtoPWM", "title": "Convert frequencies into motifs using PWMUnscaled", "topics": [ "PFMtoPWM" ] }, { "page": "plot-MotifEnrichmentReport-missing-method", "title": "Plot the motif enrichment report", "topics": [ "plot,MotifEnrichmentReport,missing-method" ] }, { "page": "plot-PWM-missing-method", "title": "Plotting for the PWM class", "topics": [ "plot,PWM,missing-method" ] }, { "page": "plotMotifScores", "title": "Plot the raw motifs scores as returned by motifScores()", "topics": [ "plotMotifScores" ] }, { "page": "plotMultipleMotifs", "title": "Plot mulitple motifs in a single plot", "topics": [ "plotMultipleMotifs" ] }, { "page": "plotPFM", "title": "Plot a PFM (not PWM) using seqLogo", "topics": [ "plotPFM" ] }, { "page": "plotTopMotifsGroup-MotifEnrichmentResults-method", "title": "Plot the top N enrichment motifs in a group of sequences", "topics": [ "plotTopMotifsGroup", "plotTopMotifsGroup,MotifEnrichmentResults-method" ] }, { "page": "plotTopMotifsSequence-MotifEnrichmentResults-method", "title": "Plot the top N enrichment motifs in a single sequence", "topics": [ "plotTopMotifsSequence", "plotTopMotifsSequence,MotifEnrichmentResults-method" ] }, { "page": "PWM-class", "title": "A class that represents a Position Weight Matrix (PWM)", "topics": [ "PWM-class" ] }, { "page": "PWMCutoffBackground-class", "title": "Hit count background distribution for a set of PWMs", "topics": [ "PWMCutoffBackground-class" ] }, { "page": "PWMEmpiricalBackground-class", "title": "Background for calculating empirical P-values", "topics": [ "PWMEmpiricalBackground-class" ] }, { "page": "PWMGEVBackground-class", "title": "Generalized Extreme Values (GEV) background for P-values", "topics": [ "PWMGEVBackground-class" ] }, { "page": "PWMLognBackground-class", "title": "Lognormal background distribution for a set of PWMs", "topics": [ "PWMLognBackground-class" ] }, { "page": "PWMUnscaled", "title": "Create a PWM from PFM", "topics": [ "PWMUnscaled" ] }, { "page": "rankingProcessAndReturn", "title": "A helper function for motifRankingForGroup and motifRankingForSequence with the common code", "topics": [ "rankingProcessAndReturn" ] }, { "page": "readJASPAR", "title": "Read motifs in JASPAR format", "topics": [ "readJASPAR" ] }, { "page": "readMotifs", "title": "Read in motifs in JASPAR or TRANSFAC format", "topics": [ "readMotifs" ] }, { "page": "readTRANSFAC", "title": "Read in motifs in TRANSFAC format", "topics": [ "readTRANSFAC" ] }, { "page": "registerCoresPWMEnrich", "title": "Register than PWMEnrich can use parallel CPU cores", "topics": [ "registerCoresPWMEnrich" ] }, { "page": "reverseComplement-PWM-method", "title": "Reverse complement for the PWM object", "topics": [ "reverseComplement,PWM-method" ] }, { "page": "scanWithPWM", "title": "Scan the whole sequence on both strands", "topics": [ "scanWithPWM" ] }, { "page": "seqLogoGrid", "title": "Draw a motif logo on an existing viewport", "topics": [ "seqLogoGrid" ] }, { "page": "sequenceReport-MotifEnrichmentResults-method", "title": "Generate a motif enrichment report for a single sequence", "topics": [ "sequenceReport", "sequenceReport,MotifEnrichmentResults-method" ] }, { "page": "show-MotifEnrichmentReport-method", "title": "show method for MotifEnrichmentReport", "topics": [ "show,MotifEnrichmentReport-method" ] }, { "page": "show-MotifEnrichmentResults-method", "title": "show method for MotifEnrichmentResults", "topics": [ "show,MotifEnrichmentResults-method" ] }, { "page": "show-PWM-method", "title": "show method for PWM", "topics": [ "show,PWM-method" ] }, { "page": "show-PWMCutoffBackground-method", "title": "show method for PWMCutoffBackground", "topics": [ "show,PWMCutoffBackground-method" ] }, { "page": "show-PWMEmpiricalBackground-method", "title": "show method for PWMEmpiricalBackground", "topics": [ "show,PWMEmpiricalBackground-method" ] }, { "page": "show-PWMGEVBackground-method", "title": "show method for PWMGEVBackground", "topics": [ "show,PWMGEVBackground-method" ] }, { "page": "show-PWMLognBackground-method", "title": "show method for PWMLognBackground", "topics": [ "show,PWMLognBackground-method" ] }, { "page": "toPWM", "title": "Convert motifs into PWMs", "topics": [ "toPWM" ] }, { "page": "tryAllMotifAlignments", "title": "Try all motif alignments and return max score", "topics": [ "tryAllMotifAlignments" ] }, { "page": "useBigMemoryPWMEnrich", "title": "If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory", "topics": [ "useBigMemoryPWMEnrich" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "evd", "gdata", "generics", "gtools", "IRanges", "S4Vectors", "Seqinfo", "seqLogo", "XVector" ], "_vignettes": [ { "source": "PWMEnrich.Rnw", "filename": "PWMEnrich.pdf", "title": "Overview of the 'PWMEnrich' package", "engine": "knitr::knitr", "headings": [], "created": "2013-10-21 18:39:58", "modified": "2015-10-01 08:58:47", "commits": 9 } ], "_score": 5.278753600952829, "_indexed": true, "_nocasepkg": "pwmenrich", "_universes": [ "bioc", "ddiez" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.49.0", "date": "2026-05-30T07:06:59.000Z", "distro": "noble", "commit": "4526a80ece5f118df1b2bc462f9c919d5671bbd9", "fileid": 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