{ "_id": "6a1b01d61d7bb097a0a008a8", "Package": "r3Cseq", "Version": "1.58.0", "Title": "Analysis of Chromosome Conformation Capture and Next-generation\nSequencing (3C-seq)", "Author": "Supat Thongjuea, MRC WIMM Centre for Computational Biology,\nWeatherall Institute of Molecular Medicine, University of\nOxford, UK ", "Maintainer": "Supat Thongjuea or\n", "Description": "This package is used for the analysis of long-range\nchromatin interactions from 3C-seq assay.", "License": "GPL-3", "URL": "http://r3cseq.genereg.net,https://github.com/supatt-lab/r3Cseq/", "Collate": "AllClasses.R AllGenerics.R Export.R FunctionInCommon.R\nFunctionsForBatchAnalysis.R RestrictionEnzymeFunctions.R\nFunctionsForNoReplicationAnalysis.R Report.R Visualize3Cseq.R\nAnnotation.R", "biocViews": "Preprocessing, Sequencing", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:35:59 UTC", "RemoteUrl": "https://github.com/bioc/r3Cseq", "RemoteRef": "RELEASE_3_23", "RemoteSha": "44c0e1529730a8a25b90e049d554572369ec6707", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:06:00 UTC", "User": "root" }, "MD5sum": "160f9f50f805f9e2f31e7a4d1ab1cdcb", "_user": "bioc-release", "_type": "src", "_file": "r3Cseq_1.58.0.tar.gz", "_fileid": "77f21d545e755c40e1d1ae1ac77fa914b3ca353ffb3a4103d6036a423a38348c", "_filesize": 4514709, "_sha256": "77f21d545e755c40e1d1ae1ac77fa914b3ca353ffb3a4103d6036a423a38348c", "_created": "2026-05-30T10:06:00.000Z", "_published": "2026-05-30T15:27:18.676Z", "_jobs": [ { "job": 78641599567, "time": 549, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307667519" }, { "job": 78641599562, "time": 758, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307686978" }, { "job": 78641599564, "time": 657, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307677926" }, { "job": 78641599583, "time": 408, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309231169" }, { "job": 78641599565, "time": 497, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309238298" }, { "job": 78640219241, "time": 666, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307400436" }, { "job": 78641599569, "time": 489, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307661631" }, { "job": 78641599576, "time": 528, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307664968" }, { "job": 78641599572, "time": 531, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307665264" }, { "job": 78641599570, "time": 537, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307665897" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/r3Cseq", "_commit": { "id": "44c0e1529730a8a25b90e049d554572369ec6707", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379759 }, "_maintainer": { "name": "Supat Thongjuea", "email": "supat.thongjuea@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "GenomicRanges", "role": "Depends" }, { "package": "Rsamtools", "role": "Depends" }, { "package": "rtracklayer", "role": "Depends" }, { "package": "VGAM", "role": "Depends" }, { "package": "qvalue", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "sqldf", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "BSgenome.Mmusculus.UCSC.mm9.masked", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10.masked", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg18.masked", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19.masked", "role": "Suggests" }, { "package": "BSgenome.Rnorvegicus.UCSC.rn5.masked", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "preprocessing", "sequencing" ], "_stars": 3, "_contributors": [ { "user": "supatt-lab", "count": 17, "uuid": 7770280 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 565, "source": "https://www.bioconductor.org/packages/stats/bioc/r3Cseq" }, "_mentions": 7, "_devurl": "https://github.com/supatt-lab/r3cseq", "_searchresults": 20, "_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/r3Cseq.html", "manual.pdf" ], "_homeurl": "https://github.com/supatt-lab/r3cseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculateBatchRPM", "calculateRPM", "contrCoverage", "contrInteractionRegions", "contrRawData", "contrRawData<-", "contrReadCount", "contrRPM", "expCoverage", "expInteractionRegions", "export3Cseq2bedGraph", "export3CseqRawReads2bedGraph", "exportBatchInteractions2text", "exportInteractions2text", "expRawData", "expRawData<-", "expReadCount", "expRPM", "generate3CseqReport", "getBatchInteractions", "getBatchRawReads", "getBatchReadCountPerRestrictionFragment", "getBatchReadCountPerWindow", "getContrInteractionsInRefseq", "getCoverage", "getExpInteractionsInRefseq", "getInteractions", "getRawReads", "getReadCountPerRestrictionFragment", "getReadCountPerWindow", "getViewpoint", "plot3Cecdf", "plotDomainogramNearViewpoint", "plotInteractionsNearViewpoint", "plotInteractionsPerChromosome", "plotOverviewInteractions" ], "_help": [ { "page": "calculateBatchRPM", "title": "calculate read per million (RPM) for replicates analysis", "topics": [ "calculateBatchRPM", "calculateBatchRPM,r3CseqInBatch-method" ] }, { "page": "calculateRPM", "title": "calculate read per million (RPM)", "topics": [ "calculateRPM", "calculateRPM,r3Cseq-method" ] }, { "page": "contrCoverage", "title": "This method has been removed.", "topics": [ "contrCoverage", "contrCoverage,r3Cseq-method" ] }, { "page": "contrInteractionRegions", "title": "get interaction regions from the control", "topics": [ "contrInteractionRegions", "contrInteractionRegions,r3CseqCommon-method" ] }, { "page": "contrRawData", "title": "Accessors for the 'contrRawData' slot of a r3Cseq object.", "topics": [ "contrRawData", "contrRawData,r3Cseq-method", "contrRawData<-", "contrRawData<-,r3Cseq-method" ] }, { "page": "contrReadCount", "title": "get read count per region for the control", "topics": [ "contrReadCount", "contrReadCount,r3CseqCommon-method" ] }, { "page": "contrRPM", "title": "get read per million (RPM) for the control", "topics": [ "contrRPM", "contrRPM,r3CseqCommon-method" ] }, { "page": "enzymeDb", "title": "Rebase The Restriction Enzyme Database", "topics": [ "enzymeDb" ] }, { "page": "expCoverage", "title": "This method has been removed.", "topics": [ "expCoverage", "expCoverage,r3Cseq-method" ] }, { "page": "expInteractionRegions", "title": "get interaction regions from the experiment", "topics": [ "expInteractionRegions", "expInteractionRegions,r3CseqCommon-method" ] }, { "page": "export3Cseq2bedGraph", "title": "export interaction regions to the 'bedGraph' format", "topics": [ "export3Cseq2bedGraph", "export3Cseq2bedGraph,r3Cseq-method" ] }, { "page": "export3CseqRawReads2bedGraph", "title": "export the interaction signal from the raw reads to the 'bedGraph' format", "topics": [ "export3CseqRawReads2bedGraph", "export3CseqRawReads2bedGraph,r3Cseq-method" ] }, { "page": "exportBatchInteractions2text", "title": "export identified interaction regions to the tab separated format for replicates analysis", "topics": [ "exportBatchInteractions2text", "exportBatchInteractions2text,r3CseqInBatch-method" ] }, { "page": "exportInteractions2text", "title": "export identified interaction regions to the tab separated format", "topics": [ "exportInteractions2text", "exportInteractions2text,r3Cseq-method" ] }, { "page": "expRawData", "title": "Accessors for the 'expRawData' slot of a r3Cseq object.", "topics": [ "expRawData", "expRawData,r3Cseq-method", "expRawData<-", "expRawData<-,r3Cseq-method" ] }, { "page": "expReadCount", "title": "get read count per region for the experiment", "topics": [ "expReadCount", "expReadCount,r3CseqCommon-method" ] }, { "page": "expRPM", "title": "get read per million (RPM) for the experiment", "topics": [ "expRPM", "expRPM,r3CseqCommon-method" ] }, { "page": "generate3CseqReport", "title": "generate reports for analysis results from r3Cseq", "topics": [ "generate3CseqReport", "generate3CseqReport,r3Cseq-method", "generate3CseqReport,r3CseqInBatch-method" ] }, { "page": "getBatchInteractions", "title": "calculate z-score, assign p-value and q-value for each interaction region for replicates data sets", "topics": [ "getBatchInteractions", "getBatchInteractions,r3CseqInBatch-method" ] }, { "page": "getBatchRawReads", "title": "Get aligned reads from the replicates BAM files", "topics": [ "getBatchRawReads", "getBatchRawReads,r3CseqInBatch-method" ] }, { "page": "getBatchReadCountPerRestrictionFragment", "title": "count reads for replicates analysis", "topics": [ "getBatchReadCountPerRestrictionFragment", "getBatchReadCountPerRestrictionFragment,r3CseqInBatch-method" ] }, { "page": "getBatchReadCountPerWindow", "title": "count reads per window size for replicates analysis", "topics": [ "getBatchReadCountPerWindow", "getBatchReadCountPerWindow,r3CseqInBatch-method" ] }, { "page": "getContrInteractionsInRefseq", "title": "identified significant interaction regions for RefSeq genes", "topics": [ "getContrInteractionsInRefseq", "getContrInteractionsInRefseq,r3Cseq-method" ] }, { "page": "getCoverage", "title": "This method has been removed.", "topics": [ "getCoverage", "getCoverage,r3Cseq-method" ] }, { "page": "getExpInteractionsInRefseq", "title": "identified significant interaction regions for RefSeq genes", "topics": [ "getExpInteractionsInRefseq", "getExpInteractionsInRefseq,r3Cseq-method" ] }, { "page": "getInteractions", "title": "calculate z-score, assign p-value and q-value for each interaction region", "topics": [ "getInteractions", "getInteractions,r3Cseq-method" ] }, { "page": "getRawReads", "title": "Get aligned reads from the BAM file", "topics": [ "getRawReads", "getRawReads,r3Cseq-method" ] }, { "page": "getReadCountPerRestrictionFragment", "title": "count reads per resitrcition fragment", "topics": [ "getReadCountPerRestrictionFragment", "getReadCountPerRestrictionFragment,r3Cseq-method" ] }, { "page": "getReadCountPerWindow", "title": "count reads per window size", "topics": [ "getReadCountPerWindow", "getReadCountPerWindow,r3Cseq-method" ] }, { "page": "getViewpoint", "title": "get the viewpoint of 3C-seq data", "topics": [ "getViewpoint", "getViewpoint,r3Cseq-method" ] }, { "page": "hg18refGene", "title": "hg18's refGenes", "topics": [ "hg18refGene" ] }, { "page": "hg19refGene", "title": "hg19's refGenes", "topics": [ "hg19refGene" ] }, { "page": "mm10refGene", "title": "mm10's refGenes", "topics": [ "mm10refGene" ] }, { "page": "mm9refGene", "title": "mm9's refGenes", "topics": [ "mm9refGene" ] }, { "page": "Myb_prom_FB", "title": "Myb_prom_FB a data set for the example of r3Cseq analysis", "topics": [ "Myb_prom_FB" ] }, { "page": "Myb_prom_FL", "title": "Myb_prom_FL a data set for the example of r3Cseq analysis", "topics": [ "Myb_prom_FL" ] }, { "page": "plot3Cecdf", "title": "This method has been removed.", "topics": [ "plot3Cecdf", "plot3Cecdf,r3Cseq-method" ] }, { "page": "plotDomainogramNearViewpoint", "title": "Plot domainogram of interaction regions near the viewpoint", "topics": [ "plotDomainogramNearViewpoint", "plotDomainogramNearViewpoint,r3Cseq-method" ] }, { "page": "plotInteractionsNearViewpoint", "title": "Plot identified interaction regions near the viewpoint", "topics": [ "plotInteractionsNearViewpoint", "plotInteractionsNearViewpoint,r3Cseq-method" ] }, { "page": "plotInteractionsPerChromosome", "title": "Plot interaction regions per each chromosome of interest", "topics": [ "plotInteractionsPerChromosome", "plotInteractionsPerChromosome,r3Cseq-method" ] }, { "page": "plotOverviewInteractions", "title": "Plot overview of identified interaction regions for genome-wide", "topics": [ "plotOverviewInteractions", "plotOverviewInteractions,r3Cseq-method" ] }, { "page": "r3Cseq-class", "title": "r3Cseq objects", "topics": [ "r3Cseq", "r3Cseq-class" ] }, { "page": "r3CseqCommon-class", "title": "r3CseqCommon objects", "topics": [ "r3CseqCommon", "r3CseqCommon-class" ] }, { "page": "r3CseqInBatch-class", "title": "r3CseqInBatch objects", "topics": [ "r3CseqInBatch", "r3CseqInBatch-class" ] }, { "page": "rn5refGene", "title": "rn5's refGenes", "topics": [ "rn5refGene" ] } ], "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "chron", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gsubfn", "gtable", "httr", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "plyr", "proto", "qvalue", "R6", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "sqldf", "stringi", "stringr", "SummarizedExperiment", "sys", "vctrs", "VGAM", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "r3Cseq.Rnw", "filename": "r3Cseq.pdf", "title": "r3Cseq", "engine": "utils::Sweave", "headings": [], "created": "2013-10-31 13:24:44", "modified": "2015-01-26 15:34:26", "commits": 4 } ], "_score": 5.100370545117563, "_indexed": false, "_nocasepkg": "r3cseq", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/r3Cseq", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.58.0", "date": "2026-05-30T10:54:53.000Z", "distro": "noble", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "f7031d12e16b549f1060a2c44bb74f0f356eea371c6cdbec14114dfe485ee019", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.6.0", "os": "linux", "version": "1.58.0", "date": "2026-05-30T10:53:50.000Z", "distro": "noble", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "b7ea3f7a6d5d516a19260e244b27d1474a99969b483fa61f9c17b31e0afc08eb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.5.3", "os": "mac", "version": "1.58.0", "date": "2026-05-30T15:23:45.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "9a238925e6cbea83bc3f27aace170675c9dbb74b1411d459e026a93110f911e1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.6.0", "os": "mac", "version": "1.58.0", "date": "2026-05-30T15:24:14.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "b4050480e271f151139517ef499033ffd44079299f5cbddf5d94aca784906128", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.6.0", "os": "wasm", "version": "1.58.0", "date": "2026-05-30T10:54:00.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "cf335a547cc220d45ab3bd2afb654217279c1cc48bbf025078e698c093839be6", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.7.0", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:51:25.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "59d0302cf2fbc964169b42e63eca6dadc0d5d6d23ee57cb87a1fcd1e7f92afad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.5.3", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:51:12.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "c7eb7f534e16165cac582467e8292dede6208f640b6b4304363361cbc04824b8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" }, { "r": "4.6.0", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:51:13.000Z", "commit": "44c0e1529730a8a25b90e049d554572369ec6707", "fileid": "f3d2e32c4f749ea324d9775e9fdc55a6037ed89cd31f4b1551a95479647cce23", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680293231" } ] }