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>

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

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")

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

Details

biocViews	AnnotationData, AnnotationHub, FunctionalAnnotation, GenomicSequence
Version	0.99.11
License	MIT + file LICENSE
Depends
Imports
Linking To
Suggests	BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges, plyranges, sessioninfo
System Requirements
Enhances
URL	https://github.com/dozmorovlab/CTCF
Bug Reports	https://github.com/dozmorovlab/CTCF/issues

Depends On Me
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Package Archives

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

Source Package	CTCF_0.99.11.tar.gz
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macOS Binary (x86_64)
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Package Short Url	https://bioconductor.org/packages/CTCF/
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