sevenC
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sevenC")Details
| Maintainer | Jonas Ibn-Salem <jonas.ibn-salem@tron-mainz.de> |
| Author | Jonas Ibn-Salem [aut, cre] |
| License | GPL-3 |
| URL | https://github.com/ibn-salem/sevenC |
| Bug Reports | https://github.com/ibn-salem/sevenC/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, ChIPSeq, ChIPchip, Classification, Coverage, DNA3DStructure, DataImport, Epigenetics, FunctionalGenomics, HiC, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/sevenC/ |
Citation
From within R, enter citation("sevenC"):
Jonas Ibn-Salem. sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. doi:10.18129/B9.bioc.sevenC, R package version 1.32.0, https://bioconductor.org/packages/sevenC.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | sevenC_1.32.0.tar.gz |
| Windows binary (x86_64) | sevenC_1.32.0.zip |
| macOS binary (arm64) | sevenC_1.32.0.tgz |
| macOS binary (x86_64) | sevenC_1.32.0.tgz |
Dependencies
Depends: R (>= 3.5), InteractionSet (>= 1.2.0)
Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), Seqinfo, 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