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sevenC

This is the development version of sevenC; for the stable release version, see sevenC.

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs


Bioconductor version: Development (3.19)

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.

Author: Jonas Ibn-Salem [aut, cre]

Maintainer: Jonas Ibn-Salem <jonas.ibn-salem at tron-mainz.de>

Citation (from within R, enter citation("sevenC")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("sevenC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sevenC")
Introduction to sevenC HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, ChIPSeq, ChIPchip, Classification, Coverage, DNA3DStructure, DataImport, Epigenetics, FunctionalGenomics, HiC, Regression, Software
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.5), InteractionSet(>= 1.2.0)
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)
System Requirements
URL https://github.com/ibn-salem/sevenC
Bug Reports https://github.com/ibn-salem/sevenC/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sevenC_1.23.0.tar.gz
Windows Binary sevenC_1.23.0.zip
macOS Binary (x86_64) sevenC_1.23.0.tgz
macOS Binary (arm64) sevenC_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sevenC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sevenC
Bioc Package Browser https://code.bioconductor.org/browse/sevenC/
Package Short Url https://bioconductor.org/packages/sevenC/
Package Downloads Report Download Stats