Package: sevenC
Type: Package
Title: Computational Chromosome Conformation Capture by Correlation of
        ChIP-seq at CTCF motifs
Version: 1.25.0
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),
        GenomeInfoDb (>= 1.12.2), 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: 6.1.0.9000
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
git_url: https://git.bioconductor.org/packages/sevenC
git_branch: devel
git_last_commit: dda512d
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.20
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 02:40:30 UTC; biocbuild
Author: Jonas Ibn-Salem [aut, cre]
Maintainer: Jonas Ibn-Salem <jonas.ibn-salem@tron-mainz.de>
Built: R 4.4.0; ; 2024-05-02 19:42:01 UTC; unix
