{ "_id": "6a4a65911e9cffeb4b833938", "Package": "GOTHiC", "Title": "Binomial test for Hi-C data analysis", "Description": "This is a Hi-C analysis package using a cumulative\nbinomial test to detect interactions between distal genomic\nloci that have significantly more reads than expected by chance\nin Hi-C experiments. It takes mapped paired NGS reads as input\nand gives back the list of significant interactions for a given\nbin size in the genome.", "Version": "1.49.0", "Date": "2025-07-22", "Author": "Borbala Mifsud and Robert Sugar", "Maintainer": "Borbala Mifsud ", "License": "GPL-3", "biocViews": "ImmunoOncology, Sequencing, Preprocessing, Epigenetics, HiC", "Config/pak/sysreqs": "make libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:28 UTC", "RemoteUrl": "https://github.com/bioc/GOTHiC", "RemoteRef": "HEAD", "RemoteSha": "1500c834235b171a69a0c7f5afd54e6206280061", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-05 13:59:09 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "GOTHiC_1.49.0.tar.gz", "_fileid": "https://r2.ropensci.org/09699759e2f6245e14c1de1ea3da4ac7f4eba3a78f2f93cfb97052ace2a31de2", "_filesize": 1753863, "_sha256": "09699759e2f6245e14c1de1ea3da4ac7f4eba3a78f2f93cfb97052ace2a31de2", "_expires": "2026-10-13T14:09:19.000Z", "_created": "2026-07-05T13:59:09.000Z", "_published": "2026-07-05T14:09:21.403Z", "_bioccheck": { "error": 3, "warning": 2, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127", "_status": "success", "_upstream": "https://github.com/bioc/GOTHiC", "_commit": { "id": "1500c834235b171a69a0c7f5afd54e6206280061", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380628 }, "_maintainer": { "name": "Borbala Mifsud", "email": "b.mifsud@qmul.ac.uk", "login": "borimifsud", "description": "", "uuid": 22659646 }, "_distro": "resolute", "_jobs": [ { "job": 85229591352, "time": 220, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8092505901" }, { "job": 85229591345, "time": 481, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8092538411" }, { "job": 85229591373, "time": 541, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8092545681" }, { "job": 85229591389, "time": 376, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8092525370" }, { "job": 85229591376, "time": 406, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8092528739" }, { "job": 85229281019, "time": 267, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8092476421" }, { "job": 85229591350, "time": 188, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8092501711" }, { "job": 85229591417, "time": 385, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8092526476" }, { "job": 85229591414, "time": 412, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8092530014" }, { "job": 85229591407, "time": 382, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8092526183" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "BSgenome", "role": "Depends" }, { "package": "data.table", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.9.38", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "ShortRead", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "HiCDataLymphoblast", "role": "Suggests" }, { "package": "parallel", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.49.0", "bioc": "3.24" }, { "branch": "release", "version": "1.48.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "preprocessing", "epigenetics", "hic" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 17, "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GOTHiC.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GOTHiC", "GOTHiChicup", "mapReadsToRestrictionSites", "pairReads" ], "_datasets": [ { "name": "filtered", "title": "A GenomicRangesList object used as an example in the GOTHiC package", "object": "lymphoid_chr20_paired_filtered", "file": "lymphoid_chr20_paired_filtered.rdata", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "filtered", "title": "A GenomicRangesList object used as an example in the GOTHiC package", "topics": [ "filtered", "lymphoid_chr20_paired_filtered" ] }, { "page": "GOTHiC", "title": "Genome Organisation Through HiC", "topics": [ "GOTHiC" ] }, { "page": "GOTHiChicup", "title": "Genome Organisation Through HiC from HiCUP output", "topics": [ "GOTHiChicup" ] }, { "page": "mapReadsToRestrictionSites", "title": "Function to map aligned and paired reads to the restriction fragments", "topics": [ "mapReadsToRestrictionSites" ] }, { "page": "pairReads", "title": "Function pairs aligned paired NGS reads", "topics": [ "pairReads" ] } ], "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bitops", "BSgenome", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "deldir", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "hwriter", "interp", "IRanges", "isoband", "jpeg", "jsonlite", "labeling", "lambda.r", "lattice", "latticeExtra", "lifecycle", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "png", "pwalign", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "ShortRead", "snow", "SparseArray", "SummarizedExperiment", "sys", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "package_vignettes.Snw", "filename": "package_vignettes.pdf", "title": "GOTHiC", "engine": "utils::Sweave", "headings": [], "created": "2013-11-19 01:22:24", "modified": "2015-05-07 14:20:55", "commits": 4 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "gothic", "_universes": [ "bioc", "borimifsud" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.49.0", "date": "2026-07-05T14:03:22.000Z", "distro": "resolute", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/e4d09e501db5f2c957c882cb1f20f432fc416767c83c5e775e4be4313e0c3a07", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.6.1", "os": "linux", "version": "1.49.0", "date": "2026-07-05T14:04:10.000Z", "distro": "resolute", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/dced25e7b8ccfbd995aa48cb8edbd749e994049cdfeeb12aa9fd43b93da7838e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.5.3", "os": "mac", "version": "1.49.0", "date": "2026-07-05T14:01:03.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/40e8a78003f9432adfc170e180ceeda01043bcbb3a59f103dde50d582bac7e59", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.6.1", "os": "mac", "version": "1.49.0", "date": "2026-07-05T14:01:52.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/4a132e40bbfd4a40a808a2ce11700e8068ad836d5d59f64c834623d74e6384f1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.6.0", "os": "wasm", "version": "1.49.0", "date": "2026-07-05T14:02:55.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/7f76a62876afd9dbea471238c281f1466beb77bb97f1c0a8298bfefb413c5881", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.7.0", "os": "win", "version": "1.49.0", "date": "2026-07-05T14:01:25.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/3d06181dc27f2aea3238d472dd35169ba7c3f2b744a20a5950dc9a4bc023e77d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.5.3", "os": "win", "version": "1.49.0", "date": "2026-07-05T14:01:34.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/08aff218e9f0511799f39ff9c857c376c35f282795f9d7ebce595ad6d941f903", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" }, { "r": "4.6.1", "os": "win", "version": "1.49.0", "date": "2026-07-05T14:01:12.000Z", "commit": "1500c834235b171a69a0c7f5afd54e6206280061", "fileid": "https://r2.ropensci.org/8e0f042cc1b0d6b20c36216db85760580e444155020cde29d3bc6bc358c4d106", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743103127" } ] }