sevenC
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see sevenC.
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Bioconductor version: 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("sevenC")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| Introduction to sevenC | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ChIPSeq, ChIPchip, Classification, Coverage, DNA3DStructure, DataImport, Epigenetics, FunctionalGenomics, HiC, Regression, Software |
| Version | 1.0.0 |
| 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 | |
| Bug Reports | https://github.com/ibn-salem/sevenC/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 | https://bioconductor.org/packages/sevenC/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |