{ "_id": "6a1b017d1d7bb097a0a004af", "Package": "seqPattern", "Title": "Visualising oligonucleotide patterns and motif occurrences\nacross a set of sorted sequences", "Version": "1.44.0", "Date": "08-05-2015", "Author": "Vanja Haberle ", "Maintainer": "Vanja Haberle ", "Description": "Visualising oligonucleotide patterns and sequence motifs\noccurrences across a large set of sequences centred at a common\nreference point and sorted by a user defined feature.", "License": "GPL-3", "biocViews": "Visualization, SequenceMatching", "Collate": "MotifScanningFunctions.R MotifScanningMethods.R\nPatternOccurrenceFunctions.R PatternOccurrenceMethods.R\nPlottingFunctions.R PlottingMethods.R", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:40:25 UTC", "RemoteUrl": "https://github.com/bioc/seqPattern", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2e938e865bc55e241a139edfe21c9b3241e96f02", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:10:25 UTC", "User": "root" }, "MD5sum": "e978633527209aa74b6293fd24789cbf", "_user": "bioc-release", "_type": "src", "_file": "seqPattern_1.44.0.tar.gz", "_fileid": "9a392ce2470058d664a48358942929e8864297d88287031c32644153fd5304a1", "_filesize": 5776493, "_sha256": "9a392ce2470058d664a48358942929e8864297d88287031c32644153fd5304a1", "_created": "2026-05-30T10:10:25.000Z", "_published": "2026-05-30T15:25:49.048Z", "_jobs": [ { "job": 78641785472, "time": 230, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307639914" }, { "job": 78641785480, "time": 273, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307644253" }, { "job": 78641785468, "time": 310, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307647980" }, { "job": 78641785478, "time": 288, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309228840" }, { "job": 78641785488, "time": 164, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309219485" }, { "job": 78640381269, "time": 343, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307421453" }, { "job": 78641785470, "time": 207, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307637695" }, { "job": 78641785503, "time": 459, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307663843" }, { "job": 78641785502, "time": 230, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307641254" }, { "job": 78641785501, "time": 234, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307641798" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/seqPattern", "_commit": { "id": "2e938e865bc55e241a139edfe21c9b3241e96f02", "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": 1777380025 }, "_maintainer": { "name": "Vanja Haberle", "email": "vanja.haberle@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "KernSmooth", "role": "Imports" }, { "package": "plotrix", "role": "Imports" }, { "package": "BSgenome.Drerio.UCSC.danRer7", "role": "Suggests" }, { "package": "CAGEr", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "parallel", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 6, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "visualization", "sequencematching" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1392, "source": "https://www.bioconductor.org/packages/stats/bioc/seqPattern" }, "_mentions": 1, "_searchresults": 15, "_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/seqPattern.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "getPatternOccurrenceList", "motifScanHits", "motifScanScores", "plotMotifDensityMap", "plotMotifOccurrenceAverage", "plotMotifScanScores", "plotPatternDensityMap", "plotPatternOccurrenceAverage" ], "_datasets": [ { "name": "TBPpwm", "title": "Position-weight matrix for TATA-box binding protein motif", "object": "TBPpwm", "file": "TBPpwm.RData", "class": [ "matrix", "array" ], "fields": {}, "rows": 4, "table": true, "tojson": true }, { "name": "zebrafishPromoters", "title": "Zebrafish promoters sequences", "object": "zebrafishPromoters", "file": "zebrafishPromoters.RData", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false }, { "name": "zebrafishPromoters24h", "title": "Zebrafish promoters genomic coordinates", "object": "zebrafishPromoters24h", "file": "zebrafishPromoters24h.RData", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "strand", "dominantTSS", "tpm", "interquantileWidth" ], "rows": 10785, "table": true, "tojson": true } ], "_help": [ { "page": "seqPattern-package", "title": "Visualising oligonucleotide patterns and motif occurences across a set of ordered sequences", "topics": [ "seqPattern-package", "seqPattern" ] }, { "page": "getPatternOccurrenceList", "title": "Occurrence of sequence patterns in a set of ordered sequences", "topics": [ "getPatternOccurrenceList", "getPatternOccurrenceList,DNAStringSet-method" ] }, { "page": "motifScanHits", "title": "Occurrence of motifs in a set of ordered sequences", "topics": [ "motifScanHits", "motifScanHits,DNAStringSet,matrix-method" ] }, { "page": "motifScanScores", "title": "Motif scanning scores for a set of ordered sequences", "topics": [ "motifScanScores", "motifScanScores,DNAStringSet,matrix-method" ] }, { "page": "plotMotifDensityMap", "title": "Plotting density maps of motif occurrence", "topics": [ "plotMotifDensityMap", "plotMotifDensityMap,DNAStringSet,matrix-method" ] }, { "page": "plotMotifOccurrenceAverage", "title": "Plotting average profile of motif occurrence", "topics": [ "plotMotifOccurrenceAverage", "plotMotifOccurrenceAverage,DNAStringSet,matrix-method" ] }, { "page": "plotMotifScanScores", "title": "Plotting heatmap of motif scanning scores", "topics": [ "plotMotifScanScores", "plotMotifScanScores,DNAStringSet,matrix-method" ] }, { "page": "plotPatternDensityMap", "title": "Plotting density maps of sequence pattern occurrence", "topics": [ "plotPatternDensityMap", "plotPatternDensityMap,DNAStringSet-method" ] }, { "page": "plotPatternOccurrenceAverage", "title": "Plotting average profile of sequence pattern occurrence", "topics": [ "plotPatternOccurrenceAverage", "plotPatternOccurrenceAverage,DNAStringSet-method" ] }, { "page": "TBPpwm", "title": "Position-weight matrix for TATA-box binding protein motif", "topics": [ "TBPpwm" ] }, { "page": "zebrafisPromoters", "title": "Zebrafish promoters sequences", "topics": [ "zebrafishPromoters" ] }, { "page": "zebrafisPromoters24h", "title": "Zebrafish promoters genomic coordinates", "topics": [ "zebrafishPromoters24h" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "generics", "GenomicRanges", "IRanges", "KernSmooth", "plotrix", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "seqPattern.Rnw", "filename": "seqPattern.pdf", "title": "seqPattern", "engine": "utils::Sweave", "headings": [], "created": "2015-01-06 21:41:27", "modified": "2015-05-08 15:29:06", "commits": 3 } ], "_score": 4.876032995097512, "_indexed": false, "_nocasepkg": "seqpattern", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/seqPattern", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.44.0", "date": "2026-05-30T10:49:57.000Z", "distro": "noble", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "167af161a0f7cc73314d1e61419fdfdf2f3b32388715a88ba18b2ffc653c1622", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.6.0", "os": "linux", "version": "1.44.0", "date": "2026-05-30T10:50:26.000Z", "distro": "noble", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "73a6ea4efe066e5e9ce9a81a317ff0902be019b6491776bc577c36bc1d8292c1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.5.3", "os": "mac", "version": "1.44.0", "date": "2026-05-30T15:23:55.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "7af64ff94afbaa31592fbff0c84d3b0077ae463b043297c440d0babd2da65f6f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.6.0", "os": "mac", "version": "1.44.0", "date": "2026-05-30T15:23:08.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "fe7ecc1e37b948558e3902ff8659ee13a16d8b43705976fc02c0544a62b502ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.6.0", "os": "wasm", "version": "1.44.0", "date": "2026-05-30T10:50:03.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "5b689569f85f5ccd1d209eecb1f53c3a8a4850467eb7617043bcf72759b1941b", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.7.0", "os": "win", "version": "1.44.0", "date": "2026-05-30T10:52:38.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "9249c5df7478110a1705d100e543a24f4054e2d7fd1c6c3b7f232515ee042978", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.5.3", "os": "win", "version": "1.44.0", "date": "2026-05-30T10:48:57.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "069a45c9ff23808013a7e753967c11736ea8bfc2ac3274e95a717269f30e3917", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" }, { "r": "4.6.0", "os": "win", "version": "1.44.0", "date": "2026-05-30T10:49:04.000Z", "commit": "2e938e865bc55e241a139edfe21c9b3241e96f02", "fileid": "6264ddf41eed21a8be4001d471d6005d1ab867cf51435315f634ee35b677ebb8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680333220" } ] }