{ "_id": "6a1ad9911d7bb097a09e762e", "Type": "Package", "Package": "EpiCompare", "Title": "Comparison, Benchmarking & QC of Epigenomic Datasets", "Version": "1.17.0", "Authors@R": "c(\nperson(given = \"Sera\", family = \"Choi\",\nemail = \"serachoi1230@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-5077-1984\")),\nperson(given=\"Brian\", family=\"Schilder\",\nemail = \"brian_schilder@alumni.brown.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-5949-2191\")),\nperson(given=\"Leyla\", family=\"Abbasova\",\nemail = \"profernitsky@gmail.com\",\nrole = \"aut\"),\nperson(given=\"Alan\", family=\"Murphy\",\nemail = \"alanmurph94@hotmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-2487-8753\")),\nperson(given=\"Nathan\", family=\"Skene\",\nemail = \"nathan.skene@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6807-3180\")),\nperson(given=\"Thomas\", family=\"Roberts\",\nemail = \"tomroberts.work15@gmail.com\",\nrole = \"ctb\"),\nperson(given=\"Hiranyamaya\", family=\"Dash\",\nemail = \"hdash.work@gmail.com\",\nrole = \"cre\",\ncomment = c(ORCID = \"0009-0005-5514-505X\"))\n)", "Description": "EpiCompare is used to compare and analyse epigenetic\ndatasets for quality control and benchmarking purposes. The\npackage outputs an HTML report consisting of three sections:\n(1. General metrics) Metrics on peaks (percentage of\nblacklisted and non-standard peaks, and peak widths) and\nfragments (duplication rate) of samples, (2. Peak overlap)\nPercentage and statistical significance of overlapping and\nnon-overlapping peaks. Also includes upset plot and (3.\nFunctional annotation) functional annotation (ChromHMM,\nChIPseeker and enrichment analysis) of peaks. Also includes\npeak enrichment around TSS.", "License": "GPL-3", "URL": "https://github.com/neurogenomics/EpiCompare", "BugReports": "https://github.com/neurogenomics/EpiCompare/issues", "VignetteBuilder": "knitr", "biocViews": "Epigenetics, Genetics, QualityControl, ChIPSeq,\nMultipleComparison, FunctionalGenomics, ATACSeq, DNaseSeq", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "FALSE", "RoxygenNote": "7.3.3", "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\nlibx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:23 UTC", "RemoteUrl": "https://github.com/bioc/EpiCompare", "RemoteRef": "HEAD", "RemoteSha": "d120a76aec49f306c918430519eeff16f9e3be4c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:52:18 UTC", "User": "root" }, "Author": "Sera Choi [aut] (ORCID: ),\nBrian Schilder [aut] (ORCID: ),\nLeyla Abbasova [aut],\nAlan Murphy [aut] (ORCID: ),\nNathan Skene [aut] (ORCID: ),\nThomas Roberts [ctb],\nHiranyamaya Dash [cre] (ORCID: )", "Maintainer": "Hiranyamaya Dash ", "MD5sum": "d692d03e3bf9ef0bf8b0df146ca66ce6", "_user": "bioc", "_type": "src", "_file": "EpiCompare_1.17.0.tar.gz", "_fileid": "135ed24c27c8fad798a83553691d0b99d47554e4054d58d5664f5d88eab46d09", "_filesize": 1548890, "_sha256": "135ed24c27c8fad798a83553691d0b99d47554e4054d58d5664f5d88eab46d09", "_created": "2026-05-30T08:52:18.000Z", "_published": "2026-05-30T12:35:29.785Z", "_jobs": [ { "job": 78637882162, "time": 596, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307034565" }, { "job": 78637882188, "time": 1193, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307092359" }, { "job": 78637882181, "time": 1224, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307095197" }, { "job": 78637882158, 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"GitHub-Actions", "_upstream": "https://github.com/bioc/EpiCompare", "_commit": { "id": "d120a76aec49f306c918430519eeff16f9e3be4c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381103 }, "_maintainer": { "name": "Hiranyamaya Dash", "email": "hdash.work@gmail.com", "login": "hdash", "uuid": 16350928 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "AnnotationHub", "role": "Imports" }, { "package": "ChIPseeker", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "genomation", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.41.3", "role": "Imports" }, { "package": "Seqinfo", "version": ">= 0.99.2", "role": "Imports" }, { "package": "GenomeInfoDb", "version": ">= 1.45.7", "role": "Imports" }, { "package": 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"SECONDARY_OR_SUPPLEMENTARY_RDS", "UNMAPPED_READS", "UNPAIRED_READ_DUPLICATES", "READ_PAIR_DUPLICATES", "READ_PAIR_OPTICAL_DUPLICATES", "PERCENT_DUPLICATION", "ESTIMATED_LIBRARY_SIZE" ], "rows": 1, "table": true, "tojson": true }, { "name": "CnT_H3K27ac", "title": "Example CUT&Tag peak file", "object": "CnT_H3K27ac", "file": "CnT_H3K27ac.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "CnT_H3K27ac_picard", "title": "Example Picard duplication metrics file 1", "object": "CnT_H3K27ac_picard", "file": "CnT_H3K27ac_picard.rda", "class": [ "data.frame" ], "fields": [ "LIBRARY", "UNPAIRED_READS_EXAMINED", "READ_PAIRS_EXAMINED", "SECONDARY_OR_SUPPLEMENTARY_RDS", "UNMAPPED_READS", "UNPAIRED_READ_DUPLICATES", "READ_PAIR_DUPLICATES", "READ_PAIR_OPTICAL_DUPLICATES", "PERCENT_DUPLICATION", "ESTIMATED_LIBRARY_SIZE" ], "rows": 1, "table": true, "tojson": true }, { "name": "encode_H3K27ac", "title": "Example ChIP-seq peak file", "object": "encode_H3K27ac", "file": "encode_H3K27ac.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "hg19_blacklist", "title": "Human genome hg19 blacklisted regions", "object": "hg19_blacklist", "file": "hg19_blacklist.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "hg38_blacklist", "title": "Human genome hg38 blacklisted regions", "object": "hg38_blacklist", "file": "hg38_blacklist.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "mm10_blacklist", "title": "Mouse genome mm10 blacklisted regions", "object": "mm10_blacklist", "file": "mm10_blacklist.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "mm9_blacklist", "title": "Mouse genome mm9 blacklisted regions", "object": "mm9_blacklist", "file": "mm9_blacklist.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "bpplapply", "title": "Wrapper for bplapply", "topics": [ "bpplapply" ] }, { "page": "check_workers", "title": "Check workers", "topics": [ "check_workers" ] }, { "page": "CnR_H3K27ac", "title": "Example CUT&Run peak file", "topics": [ "CnR_H3K27ac" ] }, { "page": "CnR_H3K27ac_picard", "title": "Example Picard duplication metrics file 2", "topics": [ "CnR_H3K27ac_picard" ] }, { "page": "CnT_H3K27ac", "title": "Example CUT&Tag peak file", "topics": [ "CnT_H3K27ac" ] }, { "page": "CnT_H3K27ac_picard", "title": "Example Picard duplication metrics file 1", "topics": [ "CnT_H3K27ac_picard" ] }, { "page": "compute_consensus_peaks", "title": "Compute consensus peaks", "topics": [ "compute_consensus_peaks" ] }, { "page": "compute_corr", "title": "Compute correlation matrix", "topics": [ "compute_corr" ] }, { "page": "download_button", "title": "Download local file", "topics": [ "download_button" ] }, { "page": "encode_H3K27ac", "title": "Example ChIP-seq peak file", "topics": [ "encode_H3K27ac" ] }, { "page": "EpiCompare", "title": "Compare epigenomic datasets", "topics": [ "EpiCompare" ] }, { "page": "fragment_info", "title": "Summary on fragments", "topics": [ "fragment_info" ] }, { "page": "gather_files", "title": "Gather files", "topics": [ "gather_files" ] }, { "page": "group_files", "title": "Group files", "topics": [ "group_files" ] }, { "page": "hg19_blacklist", "title": "Human genome hg19 blacklisted regions", "topics": [ "hg19_blacklist" ] }, { "page": "hg38_blacklist", "title": "Human genome hg38 blacklisted regions", "topics": [ "hg38_blacklist" ] }, { "page": "liftover_grlist", "title": "Liftover peak list", "topics": [ "liftover_grlist" ] }, { "page": "mm10_blacklist", "title": "Mouse genome mm10 blacklisted regions", "topics": [ "mm10_blacklist" ] }, { "page": "mm9_blacklist", "title": "Mouse genome mm9 blacklisted regions", "topics": [ "mm9_blacklist" ] }, { "page": "overlap_heatmap", "title": "Generate heatmap of percentage overlap", "topics": [ "overlap_heatmap" ] }, { "page": "overlap_percent", "title": "Calculate percentage of overlapping peaks", "topics": [ "overlap_percent" ] }, { "page": "overlap_stat_plot", "title": "Statistical significance of overlapping peaks", "topics": [ "overlap_stat_plot" ] }, { "page": "overlap_upset_plot", "title": "Generate Upset plot for overlapping peaks", "topics": [ "overlap_upset_plot" ] }, { "page": "peak_info", "title": "Summary of Peak Information", "topics": [ "peak_info" ] }, { "page": "plot_ChIPseeker_annotation", "title": "Create ChIPseeker annotation plot", "topics": [ "plot_ChIPseeker_annotation" ] }, { "page": "plot_chromHMM", "title": "Plot ChromHMM heatmap", "topics": [ "plot_chromHMM" ] }, { "page": "plot_corr", "title": "Plot correlation of peak files", "topics": [ "plot_corr" ] }, { "page": "plot_enrichment", "title": "Generate enrichment analysis plots", "topics": [ "plot_enrichment" ] }, { "page": "plot_peak_scores", "title": "Plot Peak Scores boxplot", "topics": [ "plot_peak_scores" ] }, { "page": "plot_precision_recall", "title": "Plot precision-recall curves", "topics": [ "plot_precision_recall" ] }, { "page": "precision_recall", "title": "Compute precision-recall", "topics": [ "precision_recall" ] }, { "page": "predict_precision_recall", "title": "Predict precision-recall", "topics": [ "predict_precision_recall" ] }, { "page": "rebin_peaks", "title": "Rebin peaks", "topics": [ "rebin_peaks" ] }, { "page": "report_command", "title": "Report command", "topics": [ "report_command" ] }, { "page": "report_header", "title": "Report header", "topics": [ "report_header" ] }, { "page": "tidy_peakfile", "title": "Tidy peakfiles in GRanges", "topics": [ "tidy_peakfile" ] }, { "page": "translate_genome", "title": "Translate genome", "topics": [ "translate_genome" ] }, { "page": "tss_plot", "title": "Read count frequency around TSS", "topics": [ "tss_plot" ] }, { "page": "width_boxplot", "title": "Peak width boxplot", "topics": [ "width_boxplot" ] }, { "page": "write_example_peaks", "title": "Write example peaks", "topics": [ "write_example_peaks" ] } ], "_readme": "https://github.com/bioc/EpiCompare/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "ape", "aplot", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "BSgenome", "bslib", "bsplus", "cachem", "caTools", "ChIPseeker", "cigarillo", "cli", "clipr", "cluster", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "DOSE", "downloadthis", "dplyr", "enrichit", "enrichplot", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "formatR", "fs", "futile.logger", "futile.options", "gdtools", "generics", "genomation", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggforce", "ggfun", "ggiraph", 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gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Introduction", "Data", "Installation", "Running EpiCompare", "Load package and example datasets", "Prepare input data", "Peaklist", "Blacklist", "Picard summary files", "Reference file", "Output Directory", "Run EpiCompare", "Optional plots", "Other options", "Output", "Future Enhancements", "Code used to generate the example report", "Session Information" ], "created": "2022-03-21 17:28:47", "modified": "2025-02-12 13:39:45", "commits": 19 }, { "source": "example_report.Rmd", "filename": "example_report.html", "title": "Example report", "author": "Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`", "engine": "knitr::rmarkdown", "headings": [ "EpiArchives is a public archive for interactive HTML reports generated by EpiCompare and the associated code used to create them.", "Home", "Reports", "atac_dnase_chip_example", "atac_dnase_example", "Session Information" ], "created": "2022-12-16 18:05:23", "modified": "2023-03-09 00:34:28", "commits": 5 } ], "_score": 7.622706082719948, "_indexed": true, "_nocasepkg": "epicompare", "_universes": [ "bioc", "hdash", "neurogenomics" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T09:05:10.000Z", "distro": "noble", "commit": "d120a76aec49f306c918430519eeff16f9e3be4c", "fileid": "7e85634b47b367d6a3c64bfcfb09bcd7e1fd339697dbc13b7a26966044108c85", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679503270" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T09:03:10.000Z", "distro": "noble", "commit": "d120a76aec49f306c918430519eeff16f9e3be4c", "fileid": 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