{ "_id": "6a1afad11d7bb097a09fc7b4", "Package": "sarks", "Title": "Suffix Array Kernel Smoothing for discovery of correlative\nsequence motifs and multi-motif domains", "Version": "1.25.0", "Authors@R": "person(given = \"Dennis\",\nfamily = \"Wylie\",\nrole = c(\"aut\", \"cre\"),\nemail = \"denniscwylie@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0380-3549\"))", "Description": "Suffix Array Kernel Smoothing (see\nhttps://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797),\nor SArKS, identifies sequence motifs whose presence correlates\nwith numeric scores (such as differential expression\nstatistics) assigned to the sequences (such as gene promoters).\nSArKS smooths over sequence similarity, quantified by location\nwithin a suffix array based on the full set of input sequences.\nA second round of smoothing over spatial proximity within\nsequences reveals multi-motif domains. Discovered motifs can\nthen be merged or extended based on adjacency within MMDs.\nFalse positive rates are estimated and controlled by\npermutation testing.", "biocViews": "MotifDiscovery, GeneRegulation, GeneExpression,\nTranscriptomics, RNASeq, DifferentialExpression,\nFeatureExtraction", "SystemRequirements": "Java (>= 1.8)", "License": "BSD_3_clause + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "6.1.1", "BugReports": "https://github.com/denniscwylie/sarks/issues", "URL": "https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797,\nhttps://github.com/denniscwylie/sarks", "Config/pak/sysreqs": "make default-jdk zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:02 UTC", "RemoteUrl": "https://github.com/bioc/sarks", "RemoteRef": "HEAD", "RemoteSha": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:50:28 UTC", "User": "root" }, "Author": "Dennis Wylie [aut, cre] (ORCID:\n)", "Maintainer": "Dennis Wylie ", "MD5sum": "3c72e749a4712793c9d1d3d076960b7d", "_user": "bioc", "_type": "src", "_file": "sarks_1.25.0.tar.gz", "_fileid": "2faa9c4a30e8559428adc1db7e81061d01d594af2676495ee4204e61974a51a9", "_filesize": 598447, "_sha256": "2faa9c4a30e8559428adc1db7e81061d01d594af2676495ee4204e61974a51a9", "_created": "2026-05-30T09:50:28.000Z", "_published": "2026-05-30T14:57:21.134Z", "_jobs": [ { "job": 78640788513, "time": 137, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307535683" }, { "job": 78640788509, "time": 188, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307540723" }, { "job": 78640788515, "time": 232, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307544931" }, { "job": 78640788511, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309049167" }, { "job": 78640788518, "time": 147, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309051890" }, { "job": 78640018699, "time": 179, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307310384" }, { "job": 78640788505, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307533368" }, { "job": 78640788530, "time": 141, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307533801" }, { "job": 78640788547, "time": 122, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307532720" }, { "job": 78640788546, "time": 155, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307535797" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/sarks", "_commit": { "id": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380722 }, "_maintainer": { "name": "Dennis Wylie", "email": "denniscwylie@gmail.com", "login": "denniscwylie", "description": "", "uuid": 10440117, "orcid": "0000-0003-0380-3549" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "rJava", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "binom", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "motifdiscovery", "generegulation", "geneexpression", "transcriptomics", "rnaseq", "differentialexpression", "featureextraction", "openjdk" ], "_stars": 3, "_contributors": [ { "user": "denniscwylie", "count": 192, "uuid": 10440117 }, { "user": "nturaga", "count": 8, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 338, "source": "https://www.bioconductor.org/packages/stats/bioc/sarks" }, "_devurl": "https://github.com/denniscwylie/sarks", "_searchresults": 8, "_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/readme.html", "extra/readme.md", "extra/sarks.html", "manual.pdf" ], "_homeurl": "https://github.com/denniscwylie/sarks", "_realowner": "bioc", "_cranurl": false, "_exports": [ "blockInfo", "blockScores", "clusterCounts", "clusterKmers", "estimateFalsePositiveRate", "extendKmers", "kmerCounts", "kmerPeaks", "locateClusters", "locateKmers", "mergedKmerSubPeaks", "permutationDistribution", "permutationThresholds", "pruneIntervals", "regexCounts", "regexLocate", "Sarks", "sarksFilters", "sourceBlock" ], "_datasets": [ { "name": "simulatedScores", "title": "Scores associated with simulated sequences from SArKS paper.", "object": "simulatedScores", "file": "simulatedScores.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "simulatedSeqs", "title": "Simulated sequences from SArKS paper.", "object": "simulatedSeqs", "file": "simulatedSeqs.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "blockInfo", "title": "Get sarks smoothed scores for input sequence", "topics": [ "blockInfo" ] }, { "page": "blockScores", "title": "SArKS input scores", "topics": [ "blockScores" ] }, { "page": "clusterCounts", "title": "Count occurrences of k-mer clusters", "topics": [ "clusterCounts" ] }, { "page": "clusterKmers", "title": "Cluster k-mers", "topics": [ "clusterKmers" ] }, { "page": "estimateFalsePositiveRate", "title": "Estimating SArKS false positive rate", "topics": [ "estimateFalsePositiveRate" ] }, { "page": "extendKmers", "title": "Extend k-mers in length where possible", "topics": [ "extendKmers" ] }, { "page": "kmerCounts", "title": "Count occurrences of k-mer", "topics": [ "kmerCounts" ] }, { "page": "kmerPeaks", "title": "Call k-mer peaks", "topics": [ "kmerPeaks" ] }, { "page": "locateClusters", "title": "Locate occurrences of specified clusters of k-mers", "topics": [ "locateClusters" ] }, { "page": "locateKmers", "title": "Locate occurrences of specified k-mers", "topics": [ "locateKmers" ] }, { "page": "mergedKmerSubPeaks", "title": "Identify and merge k-mer sub-peaks within multi-motif domains", "topics": [ "mergedKmerSubPeaks" ] }, { "page": "permutationDistribution", "title": "Estimating distribution of maximum smoothed sequence scores under permutation", "topics": [ "permutationDistribution" ] }, { "page": "permutationThresholds", "title": "Set smoothed score thresholds based on permutation distribution", "topics": [ "permutationThresholds" ] }, { "page": "pruneIntervals", "title": "Prune nested k-mer intervals from called k-mer peak set.", "topics": [ "pruneIntervals" ] }, { "page": "regexCounts", "title": "Count occurrences of regular expression", "topics": [ "regexCounts" ] }, { "page": "regexLocate", "title": "Locate occurrences of regular expression", "topics": [ "regexLocate" ] }, { "page": "Sarks", "title": "Suffix Array Kernel Smoothing", "topics": [ "Sarks" ] }, { "page": "sarksFilters", "title": "Smoothing window and Gini impurity filter settings", "topics": [ "sarksFilters" ] }, { "page": "simulatedScores", "title": "Scores associated with simulated sequences from SArKS paper.", "topics": [ "simulatedScores" ] }, { "page": "simulatedSeqs", "title": "Simulated sequences from SArKS paper.", "topics": [ "simulatedSeqs" ] }, { "page": "sourceBlock", "title": "Identify associated input sequence for given position(s) in suffix array", "topics": [ "sourceBlock" ] } ], "_readme": "https://github.com/bioc/sarks/raw/HEAD/README.md", "_rundeps": [ "binom", "BiocGenerics", "Biostrings", "cluster", "crayon", "generics", "IRanges", "rJava", "S4Vectors", "Seqinfo", "XVector" ], "_sysdeps": [ { "shlib": "libjvm", "package": "openjdk-21-jre-headless", "headers": "openjdk-21-jre-headless", "source": "openjdk", "version": "21.0.11+10-1~24.04.2", "name": "openjdk", "homepage": "https://openjdk.java.net/", "description": "OpenJDK Java runtime, using Hotspot JIT (headless)" } ], "_vignettes": [ { "source": "sarks-vignette.Rnw", "filename": "sarks-vignette.pdf", "title": "sarks-vignette", "engine": "utils::Sweave", "headings": [], "created": "2020-02-13 16:00:04", "modified": "2022-02-24 18:44:23", "commits": 11 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "sarks", "_universes": [ "bioc", "denniscwylie" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T10:32:32.000Z", "distro": "noble", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "1934e0996d7da183c3d23a31cad706aca7fd22f9ecce6406df62c62f6377630d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T10:33:08.000Z", "distro": "noble", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "1643624cc2b6b790cdd87f3f08fc78990b96273cd560de771a919fc339f337e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T14:55:54.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "50beace64644abef3e97a7b0e0a91a66a08a4eb975403aff15a65e9a26bbae6d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T14:56:09.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "625a88f9eee55aea96c47e625c06e180d5391af3008c7f81eff03dac39cd9c7e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T10:32:12.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "2b4ba0a44c4990464c09ed7540c9d62a4cf901f6ef133db0beb7d5494853ec72", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:31:07.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "4ba293831e1b4ce610ac79239b06284c220009a57427cfd34a8f5db6a71839a0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:30:59.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "9d76864a7e23a04f97fe51b6a31d3dda2343d1c6860583b26b8f6d0586309ad0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:31:40.000Z", "commit": "14425d46040248f81ae07b9c8bf8f61286cb18ac", "fileid": "16faeeaca77be098e7152cbfa6faa846100cd187689f405342d3c6853bf8d1d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677209099" } ] }