{ "_id": "6ae765429ceaa78f20099fcd", "Package": "epiSeeker", "Type": "Package", "Title": "epiSeeker: an R package for Annotation, Comparison and\nVisualization of multi-omics epigenetic data", "Version": "1.1.4", "Authors@R": "c(\nperson(given = \"Guangchuang\", family = \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\", \"fnd\"), comment = c(ORCID = \"0000-0002-6485-8781\")),\nperson(given = \"Ming\", family = \"Li\", email = \"limiang929@gmail.com\", role = \"ctb\"),\nperson(given = \"Qianwen\", family = \"Wang\", email = \"treywea@gmail.com\", role = \"ctb\"),\nperson(given = \"Yun\", family = \"Yan\", email = \"youryanyun@gmail.com\", role = \"ctb\"),\nperson(given = \"Hervé\", family = \"Pagès\", email = \"hpages.on.github@gmail.com\", role = \"ctb\"),\nperson(given = \"Michael\", family = \"Kluge\", email = \"michael.kluge@bio.ifi.lmu.de\", role = \"ctb\"),\nperson(given = \"Thomas\", family = \"Schwarzl\", email = \"schwarzl@embl.de\", role = \"ctb\"),\nperson(given = \"Zhougeng\", family = \"Xu\", email = \"xuzhougeng@163.com\", role = \"ctb\"),\nperson(given = \"Chun-Hui\", family = \"Gao\", email = \"gaospecial@gmail.com\", role = \"ctb\")\n)", "Description": "This package implements functions to analyze multi-omics\nepigenetic data. Data of fragment type and base type are\nsupported by epiSeeker. It provides functions to retrieve the\nnearest genes around the peak, annotate genomic region of the\npeak, statistical methods to estimate the significance of\noverlap among peak data sets, and motif analysis. It\nincorporates the GEO database for users to compare their own\ndataset with those deposited in the database. The comparison\ncan be used to infer cooperative regulation and thus can be\nused to generate hypotheses. Several visualization functions\nare implemented to summarize the coverage of the peak\nexperiment, average profile and heatmap of peaks binding to TSS\nregions, genomic annotation, distance to TSS, overlap of peaks\nor genes, and the single-base resolution epigenetic data by\nconsidering the strand, motif, and additional information.", "URL": "https://github.com/YuLab-SMU/epiSeeker", "BugReports": "https://github.com/YuLab-SMU/epiSeeker/issues", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "ByteCompile": "true", "License": "Artistic-2.0", "biocViews": "Annotation, ChIPSeq, Software, Visualization,\nMultipleComparison, Coverage, MotifAnnotation, GeneRegulation", "LazyData": "false", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-05 10:09:52 UTC", "RemoteUrl": "https://github.com/bioc/epiSeeker", "RemoteRef": "HEAD", "RemoteSha": "c276887fd480420c4d0f43121fa42a7ed2730179", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 13:38:04 UTC", "User": "root" }, "Author": "Guangchuang Yu [aut, cre, fnd] (ORCID:\n),\nMing Li [ctb],\nQianwen Wang [ctb],\nYun Yan [ctb],\nHervé Pagès [ctb],\nMichael Kluge [ctb],\nThomas Schwarzl [ctb],\nZhougeng Xu [ctb],\nChun-Hui Gao [ctb]", "Maintainer": "Guangchuang Yu ", "_user": "bioc", "_type": "src", "_file": "epiSeeker_1.1.4.tar.gz", "_fileid": "https://r2.ropensci.org/7b63c9a2ed7c0bf4ffd3b7264de3f49cde4e4772bcac8f8a68bd4878a2a98ac0", "_filesize": 9558067, "_sha256": "7b63c9a2ed7c0bf4ffd3b7264de3f49cde4e4772bcac8f8a68bd4878a2a98ac0", "_expires": "2027-02-09T16:13:51.000Z", "_created": "2026-11-01T13:38:04.000Z", "_published": "2026-11-01T16:13:53.981Z", "_upstream": "https://github.com/bioc/epiSeeker", "_status": "success", "_maintainer": { "name": "Guangchuang Yu", "email": "guangchuangyu@gmail.com", "login": "guangchuangyu", "twitter": "@guangchuangyu", "description": "Professor of Bioinformatics at Southern Medical University.", "uuid": 626539, "orcid": "0000-0002-6485-8781" }, "_jobs": [ { "job": 124865034712, "time": 318, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13087380610" }, { "job": 124865034687, "time": 1011, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13087541058" }, { "job": 124865034716, "time": 829, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13087102707" }, { "job": 124865034738, "time": 824, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13091185483" }, { "job": 124865036282, "time": 856, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13090423259" }, { "job": 124859164493, "time": 473, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13086455173" }, { "job": 124865034677, "time": 313, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13086669130" }, { "job": 124865034685, "time": 838, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13085503930" }, { "job": 124865034723, "time": 681, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13085754599" }, { "job": 124865034680, "time": 829, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13086467945" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309773076", "_commit": { "id": "c276887fd480420c4d0f43121fa42a7ed2730179", "author": "Guangchuang Yu ", "committer": "Guangchuang Yu ", "message": "handle an empty peak set instead of failing with an unrelated error\n\nannotateSeq(GRanges(), TxDb = txdb) failed with \"Error: invalid subscript\",\nthe same root cause as #238: follow()/precede() return a SortedByQueryHits\nobject rather than indices for an empty query, which is not a valid row\nsubscript. annotateSeq() now returns an empty csAnno (0 rows, peakNum 0, empty\ndetailGenomicAnnotation and annoStat) before the steps that are not defined for\nzero peaks.\n\nNote: unlike ChIPseeker, getNearestFeatureIndicesAndDistances() here is left\nuntouched, so seq2gene() still fails on an empty input; the guard belongs to the\nshared helper and can be added when the two packages are next synchronised.\n", "time": 1791194992 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "aplot", "role": "Imports" }, { "package": "bsseq", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "boot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" 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parameter method", "topics": [ "check_bin" ] }, { "page": "check_extension", "title": "check upstream and downstream extension", "topics": [ "check_extension" ] }, { "page": "check_windows", "title": "check windows function", "topics": [ "check_windows" ] }, { "page": "combine_csAnno", "title": "combine_csAnno", "topics": [ "combine_csAnno" ] }, { "page": "create_regex_patterns_negative", "title": "create regex patterns in negative strand", "topics": [ "create_regex_patterns_negative" ] }, { "page": "create_regex_patterns_positive", "title": "create regex patterns in positive strand", "topics": [ "create_regex_patterns_positive" ] }, { "page": "csAnno-class", "title": "Class \"csAnno\" This class represents the output of epiSeeker Annotation", "topics": [ "csAnno-class", "plotAnnoBar,csAnno-method", "plotAnnoPie,csAnno-method", "plotDistToTSS,csAnno-method", "show,csAnno-method", "subset,csAnno-method", "upsetplot,csAnno-method", "vennpie,csAnno-method" ] }, { "page": "demo_bmdata", "title": "demo base modification data", "topics": [ "demo_bmdata" ] }, { "page": "demo_peak", "title": "demo peak file", "topics": [ "demo_peak" ] }, { "page": "downloadGEObedFiles", "title": "downloadGEObedFiles", "topics": [ "downloadGEObedFiles" ] }, { "page": "downloadGSMbedFiles", "title": "downloadGSMbedFiles", "topics": [ "downloadGSMbedFiles" ] }, { "page": "dropAnno", "title": "dropAnno", "topics": [ "dropAnno" ] }, { "page": "enrichAnnoOverlap", "title": "enrichAnnoOverlap", "topics": [ "enrichAnnoOverlap" ] }, { "page": "enrichPeakOverlap", "title": "enrichPeakOverlap", "topics": [ "enrichPeakOverlap" ] }, { "page": "epiSeekerCache", "title": "Name of the epiSeeker cache environment (internal static variable)", "topics": [ "epiSeekerCache" ] }, { "page": "extend_gr", "title": "Extend regions functions", "topics": [ "extend_gr" ] }, { "page": "filter.GRanges", "title": "Extend filter to Peak (GRanges class object)", "topics": [ "filter.GRanges" ] }, { "page": "getAnnoStat", "title": "getAnnoStat", "topics": [ "getAnnoStat" ] }, { "page": "getBioRegion", "title": "Prepare a bioregion of selected feature", "topics": [ "getBioRegion" ] }, { "page": "getBmMatrix-methods", "title": "getBmMatrix methods generics", "topics": [ "bmData-methods", "BSseq-methods", "getBmMatrix", "getBmMatrix,", "getBmMatrix,ANY,bmData-method", "getBmMatrix,ANY,BSseq-method" ] }, { "page": "getBmMatrix.bmData", "title": "get the information of base modification", "topics": [ "getBmMatrix.bmData" ] }, { "page": "getBmMatrix.BSseq", "title": "Get the information of base modification", "topics": [ "getBmMatrix.BSseq" ] }, { "page": "getGeneAnno", "title": "getGeneAnno", "topics": [ "getGeneAnno" ] }, { "page": "getGenomicAnnotation", "title": "getGenomicAnnotation", "topics": [ "getGenomicAnnotation" ] }, { "page": "getGEOgenomeVersion", "title": "getGEOgenomeVersion", "topics": [ "getGEOgenomeVersion" ] }, { "page": "getGEOInfo", "title": "getGEOInfo", "topics": [ "getGEOInfo" ] }, { "page": "getGEOspecies", "title": "getGEOspecies", "topics": [ "getGEOspecies" ] }, { "page": "getMotifMatrix", "title": "Get the information of motif in a range", "topics": [ "getMotifMatrix" ] }, { "page": "getNearestFeatureIndicesAndDistances", "title": "getNearestFeatureIndicesAndDistances", "topics": [ "getNearestFeatureIndicesAndDistances" ] }, { "page": "getPromoters", "title": "Get promoter region in GRanges format", "topics": [ "getPromoters" ] }, { "page": "getSampleFiles", "title": "getSampleFiles", "topics": [ "getSampleFiles" ] }, { "page": "getTagMatrix", "title": "getTagMatrix", "topics": [ "getTagMatrix" ] }, { "page": "getTagMatrix_body", "title": "getTagMatrix function for region of body", "topics": [ "getTagMatrix_body" ] }, { "page": "getTagMatrix_body_internal", "title": "get tagmatrix internal function", "topics": [ "getTagMatrix_body_internal" ] }, { "page": "getTagMatrix_site", "title": "getTagMatrix function for region of site", "topics": [ "getTagMatrix_site" ] }, { "page": "getTagMatrix.internal", "title": "getTagMatrix internal function", "topics": [ "getTagMatrix.internal" ] }, { "page": "grange2mt", "title": "change a list grange object to matrix", "topics": [ "grange2mt" ] }, { "page": "gsminfo", "title": "Information Datasets", "topics": [ "gsminfo", "ucsc_release" ] }, { "page": "loadTxDb", "title": "load defaulst txdb", "topics": [ "loadTxDb" ] }, { "page": "makeBmDataFromData-methods", "title": "makeBmDataFromData method generics", "topics": [ "makeBmDataFromData", "makeBmDataFromData,CompressedGRangesList-method", "makeBmDataFromData,data.frame-method", "makeBmDataFromData,GRanges-method", "makeBmDataFromData,list-method" ] }, { "page": "makeBmDataFromData", "title": "makeBmDataFromData.internal", "topics": [ "makeBmDataFromData.internal" ] }, { "page": "makeBmDataFromFiles", "title": "make bmData from files", "topics": [ "makeBmDataFromFiles" ] }, { "page": "mutate.GRanges", "title": "Extend mutate to Peak (GRanges class 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"plotCov", "topics": [ "plotCov" ] }, { "page": "plotDistToTSS-methods", "title": "plotDistToTSS method generics", "topics": [ "plotDistToTSS", "plotDistToTSS,csAnno,ANY-method", "plotDistToTSS,list-method" ] }, { "page": "plotDistToTSS.data.frame", "title": "plotDistToTSS.data.frame", "topics": [ "plotDistToTSS.data.frame" ] }, { "page": "plotGeneTrack", "title": "Plot gene track", "topics": [ "plotGeneTrack" ] }, { "page": "plotMotifProf", "title": "Plot the profile of motif of specific peak", "topics": [ "plotMotifProf" ] }, { "page": "plotPeakHeatmap", "title": "plotPeakHeatmap function", "topics": [ "plotPeakHeatmap" ] }, { "page": "plotPeakHeatmap_sub", "title": "Plot peak heatmap sub function", "topics": [ "plotPeakHeatmap_sub" ] }, { "page": "plotPeakHeatmap_sub.internal", "title": "internal function of plotPeakHeatmap", "topics": [ "plotPeakHeatmap_sub.internal" ] }, { "page": "plotPeakProf", "title": "plot peak profile", "topics": [ "plotPeakProf" ] }, { "page": "pwm_obj", 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