Package: sevenC Type: Package Title: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs Version: 1.33.0 Authors@R: person("Jonas", "Ibn-Salem", email = "jonas.ibn-salem@tron-mainz.de", role = c("aut", "cre")) Description: Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes. License: GPL-3 Encoding: UTF-8 LazyData: TRUE Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), Seqinfo, GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr Depends: R (>= 3.5), InteractionSet (>= 1.2.0) RoxygenNote: 7.3.3 URL: https://github.com/ibn-salem/sevenC biocViews: DNA3DStructure, ChIPchip, Coverage, DataImport, Epigenetics, FunctionalGenomics, Classification, Regression, ChIPSeq, HiC, Annotation VignetteBuilder: knitr BugReports: https://github.com/ibn-salem/sevenC/issues Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev libx11-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: 2026-07-18 04:46:51 UTC; root Author: Jonas Ibn-Salem [aut, cre] Maintainer: Jonas Ibn-Salem