{ "_id": "6a1ee933b401979e73411c87", "Package": "epiSeeker", "Type": "Package", "Title": "epiSeeker: an R package for Annotation, Comparison and\nVisualization of multi-omics epigenetic data", "Version": "1.1.0", "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", "RoxygenNote": "7.3.3", "LazyData": "false", "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": "2026-04-28 13:06:06 UTC", "RemoteUrl": "https://github.com/bioc/epiSeeker", "RemoteRef": "HEAD", "RemoteSha": "03bc0c589981d5ed5f1109d7517bca6e1f613bac", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-19 10:25:38 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 ", "MD5sum": "dfedf2141be34daa5bee8f7cf7dc570c", "_user": "bioc", "_type": "src", "_file": "epiSeeker_1.1.0.tar.gz", "_fileid": "171efb87fd06edf48bb310c0901bb3507e36be1e48c2f6695fa778dc72554bd4", "_filesize": 9444876, "_sha256": "171efb87fd06edf48bb310c0901bb3507e36be1e48c2f6695fa778dc72554bd4", "_created": "2026-05-19T10:25:38.000Z", "_published": "2026-06-02T14:31:15.454Z", "_jobs": [ { "job": 79094245682, "time": 395, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7081066969" }, { "job": 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regions", "Profile of one sample of one reference region", "Visualization of base modification", "Visualization of gene track", "Visualization of motif", "Peak Annotation", "Visualize Genomic Annotation", "Visualize distribution of TF-binding loci relative to TSS", "Functional enrichment analysis", "ChIP peak data set comparison", "ChIP peak annotation comparision", "Functional profiles comparison", "Overlap of peaks and annotated genes", "Statistical testing of ChIP seq overlap", "Shuffle genome coordination", "Peak overlap enrichment analysis", "Data Mining with ChIP seq data deposited in GEO", "GEO data collection", "Download GEO ChIP data sets", "Overlap significant testing", "Need helps?", "Session Information", "References" ], "created": "2025-09-18 15:27:29", "modified": "2026-01-07 06:41:08", "commits": 6 } ], "_score": 5.146128035678238, "_indexed": true, "_nocasepkg": "episeeker", "_universes": [ "bioc", "guangchuangyu", "yulab-smu" ], "_binaries": [ { "r": "4.7.0", "os": 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