{ "_id": "6ac61d5cf511ae58c09a653d", "Package": "ChIPseeker", "Type": "Package", "Title": "ChIPseeker for ChIP peak Annotation, Comparison, and\nVisualization", "Version": "1.49.3", "Authors@R": "c( \nperson(given = \"Guangchuang\", family = \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), 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\", comment=c(ORCID = \"0000-0002-1445-7939\"))\n)", "Maintainer": "Guangchuang Yu ", "Description": "This package implements functions to retrieve the nearest\ngenes around the peak, annotate genomic region of the peak,\nstatstical methods for estimate the significance of overlap\namong ChIP peak data sets, and incorporate GEO database for\nuser to compare the own dataset with those deposited in\ndatabase. The comparison can be used to infer cooperative\nregulation and thus can be used to generate hypotheses. Several\nvisualization functions are implemented to summarize the\ncoverage of the peak experiment, average profile and heatmap of\npeaks binding to TSS regions, genomic annotation, distance to\nTSS, and overlap of peaks or genes.", "Remotes": [ "GuangchuangYu/enrichplot" ], "URL": "https://yulab-smu.top/contribution-knowledge-mining/", "BugReports": "https://github.com/YuLab-SMU/ChIPseeker/issues", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "ByteCompile": "true", "License": "Artistic-2.0", "biocViews": "Annotation, ChIPSeq, Software, Visualization,\nMultipleComparison", "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 10:09:17 UTC", "RemoteUrl": "https://github.com/bioc/ChIPseeker", "RemoteRef": "HEAD", "RemoteSha": 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"id": "df67ad44b3d5772439fb74d6c66fb6751bc14e7a", "author": "Guangchuang Yu ", "committer": "Guangchuang Yu ", "message": "handle an empty peak set instead of failing with unrelated errors\n\nannotatePeak(GRanges(), TxDb = txdb) failed with \"Error: invalid subscript\"\nand, with addFlankGeneInfo, with \"replacement has 1 row, data has 0\".\n\nRoot cause is the same as in #238: for an empty query follow()/precede()\nreturn a SortedByQueryHits object rather than indices, which is not a valid row\nsubscript. getNearestFeatureIndicesAndDistances() now returns empty index,\ndistance and peak vectors in that case, and annotatePeak() returns an empty\ncsAnno (0 rows, peakNum 0, empty detailGenomicAnnotation and annoStat) before\nthe steps that are not defined for zero peaks. seq2gene() returns\ncharacter(0) for an empty input as a result of the same guard.\n\nCovered for the plain call and for addFlankGeneInfo + annoDb.\n", "time": 1791194957 }, "_maintainer": { "name": "Guangchuang Yu", 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