sevenC

DOI: 10.18129/B9.bioc.sevenC    

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

Bioconductor version: Release (3.7)

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 <j.ibn-salem at uni-mainz.de>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("sevenC")

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 1.0.0
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
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_1.0.0.tar.gz
Windows Binary sevenC_1.0.0.zip
Mac OS X 10.11 (El Capitan) sevenC_1.0.0.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 http://bioconductor.org/packages/sevenC/
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