{ "_id": "6a1afa7d1d7bb097a09fc06d", "Package": "sevenC", "Type": "Package", "Title": "Computational Chromosome Conformation Capture by Correlation of\nChIP-seq at CTCF motifs", "Version": "1.33.0", "Authors@R": "person(\"Jonas\", \"Ibn-Salem\", email = \"jonas.ibn-salem@tron-mainz.de\", \nrole = c(\"aut\", \"cre\"))", "Description": "Chromatin looping is an essential feature of eukaryotic\ngenomes and can bring regulatory sequences, such as enhancers\nor transcription factor binding sites, in the close physical\nproximity of regulated target genes. Here, we provide sevenC,\nan R package that uses protein binding signals from ChIP-seq\nand sequence motif information to predict chromatin looping\nevents. Cross-linking of proteins that bind close to loop\nanchors result in ChIP-seq signals at both anchor loci. These\nsignals are used at CTCF motif pairs together with their\ndistance and orientation to each other to predict whether they\ninteract or not. The resulting chromatin loops might be used to\nassociate enhancers or transcription factor binding sites\n(e.g., ChIP-seq peaks) to regulated target genes.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "TRUE", "RoxygenNote": "7.3.3", "URL": "https://github.com/ibn-salem/sevenC", "biocViews": "DNA3DStructure, ChIPchip, Coverage, DataImport, Epigenetics,\nFunctionalGenomics, Classification, Regression, ChIPSeq, HiC,\nAnnotation", "VignetteBuilder": "knitr", "BugReports": "https://github.com/ibn-salem/sevenC/issues", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:53 UTC", "RemoteUrl": "https://github.com/bioc/sevenC", "RemoteRef": "HEAD", "RemoteSha": "d7e339d67a083e760e9eb2a247e64a320b21d77f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:49:37 UTC", "User": "root" }, "Author": "Jonas Ibn-Salem [aut, cre]", "Maintainer": "Jonas Ibn-Salem ", "MD5sum": "3a7127f1efd1a56203753dfa8a9623ef", "_user": "bioc", "_type": "src", "_file": "sevenC_1.33.0.tar.gz", "_fileid": "f23bde763d03a0c18dffd92f8736ae7a0b2cb9e4281c735c77b2e5ba78aac2d2", "_filesize": 1931382, "_sha256": "f23bde763d03a0c18dffd92f8736ae7a0b2cb9e4281c735c77b2e5ba78aac2d2", "_created": "2026-05-30T09:49:37.000Z", "_published": "2026-05-30T14:55:57.257Z", "_jobs": [ { "job": 78640756582, "time": 176, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307531582" }, { "job": 78640756591, "time": 374, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307550253" }, { "job": 78640756590, "time": 401, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307552382" }, { "job": 78640756601, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309043562" }, { "job": 78640756603, "time": 167, "config": "macos-release-arm64", "r": "4.6.0", 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x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380473 }, "_maintainer": { "name": "Jonas Ibn-Salem", "email": "jonas.ibn-salem@tron-mainz.de", "login": "ibn-salem", "description": "", "uuid": 1645130 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "InteractionSet", "version": ">= 1.2.0", "role": "Depends" }, { "package": "rtracklayer", "version": ">= 1.34.1", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.22.0", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.28.5", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.10.3", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.14.4", "role": "Imports" }, { "package": "readr", "version": ">= 1.1.0", "role": "Imports" }, { "package": "purrr", "version": ">= 0.2.2", "role": "Imports" }, { "package": "data.table", 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{ "page": "getCisPairs", "title": "Build a 'GInteractions' object with all pairs of input 'GRanges' within a given distance.", "topics": [ "getCisPairs" ] }, { "page": "modelBest10Avg", "title": "Default parameters for logistic regression model in sevenC.", "topics": [ "modelBest10Avg" ] }, { "page": "motif.hg19.CTCF", "title": "CTCF motif locations in human genome hg19.", "topics": [ "motif.hg19.CTCF" ] }, { "page": "motif.hg19.CTCF.chr22", "title": "CTCF motif locations on chromosome 22 in human genome hg19.", "topics": [ "motif.hg19.CTCF.chr22" ] }, { "page": "motif.hg19.CTCF.chr22.cov", "title": "CTCF motifs on human chromosome 22 with example coverage.", "topics": [ "motif.hg19.CTCF.chr22.cov" ] }, { "page": "parseLoopsRao", "title": "Parse chromatin loops from Rao et al. 2014 as strict 'GInteractions'.", "topics": [ "parseLoopsRao" ] }, { "page": "parseLoopsTang", "title": "Parse chromatin interactions from Tang et al. 2015 as 'GInteractions'.", "topics": [ "parseLoopsTang" ] }, 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and compute correaltion", "Predict loops", "More detailed usage example", "Prepare CTCF motif pairs", "Add ChIP-seq signals at motifs sites", "Build pairs of motifs as candidate interactions", "Compute ChIP-seq similarity at motif pairs", "Downstream analysis with predicted chromatin loops", "Linking sets of regions", "Write predicted loops to an output file", "Train prediction model using custom data", "Prepare motif pairs and add ChIP-seq data", "Train predictor with known loops", "Train logistic regression model", "Predict loops with a custom model", "Session info", "References" ], "created": "2018-01-24 14:08:36", "modified": "2018-09-08 22:39:42", "commits": 9 } ], "_score": 6.113943352306837, "_indexed": true, "_nocasepkg": "sevenc", "_universes": [ "bioc", "ibn-salem" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-05-30T10:32:34.000Z", "distro": "noble", "commit": "d7e339d67a083e760e9eb2a247e64a320b21d77f", "fileid": 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