sevenC

DOI: 10.18129/B9.bioc.sevenC    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	Introduction to sevenC
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPSeq, ChIPchip, Classification, Coverage, DNA3DStructure, DataImport, Epigenetics, FunctionalGenomics, HiC, Regression, Software
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 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)
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr
SystemRequirements
Enhances
URL	https://github.com/ibn-salem/sevenC
BugReports	https://github.com/ibn-salem/sevenC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	sevenC_1.12.0.tar.gz
Windows Binary	sevenC_1.12.0.zip
macOS 10.13 (High Sierra)	sevenC_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sevenC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sevenC
Package Short Url	https://bioconductor.org/packages/sevenC/
Package Downloads Report	Download Stats