Package: sevenC
Type: Package
Title: Computational Chromosome Conformation Capture by Correlation of
        ChIP-seq at CTCF motifs
Version: 1.30.0
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
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:45:03 UTC
RemoteUrl: https://github.com/bioc/sevenC
RemoteRef: RELEASE_3_22
RemoteSha: c38ab75bb1c786968497aee691ccd3e0ce5d9c1c
NeedsCompilation: no
Packaged: 2025-11-11 17:43:08 UTC; root
Author: Jonas Ibn-Salem [aut, cre]
Maintainer: Jonas Ibn-Salem <jonas.ibn-salem@tron-mainz.de>
Built: R 4.5.2; ; 2025-11-11 17:53:57 UTC; windows
