CTCF

DOI: 10.18129/B9.bioc.CTCF  

Genomic coordinates of CTCF binding sites, with orientation

Bioconductor version: Release (3.17)

Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. CTCF sites obtained using JASPAR's MA0139.1 PWM and filtered at 1e-6 p-value threshold are recommended.

Author: Mikhail Dozmorov [aut, cre] , Eric Davis [aut], Wancen Mu [aut], Stuart Lee [aut], Tim Triche [aut], Douglas Phanstiel [aut], Michael Love [aut]

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("CTCF")

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("CTCF")

 

HTML	R Script	Introduction to CTCF
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AnnotationData, AnnotationHub, FunctionalAnnotation, GenomicSequence
Version	0.99.11
License	MIT + file LICENSE
Depends
Imports
LinkingTo
Suggests	BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges, plyranges, sessioninfo
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/CTCF
BugReports	https://github.com/dozmorovlab/CTCF/issues
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	CTCF_0.99.11.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url	https://bioconductor.org/packages/CTCF/
Package Downloads Report	Download Stats