DESCRIPTION

Package: CTCF
Title: Genomic coordinates of CTCF binding sites, with orientation
Version: 0.99.11
Authors@R: c(
    person(given = "Mikhail",
           family = "Dozmorov",
           role = c("aut", "cre"),
           email = "mikhail.dozmorov@gmail.com",
           comment = c(ORCID = "0000-0002-0086-8358")),
    person(given = "Eric",
           family = "Davis",
           role = c("aut")),
    person(given = "Wancen",
           family = "Mu",
           role = c("aut")),
    person(given = "Stuart",
           family = "Lee",
           role = c("aut")),
    person(given = "Tim",
           family = "Triche",
           role = c("aut")),
    person(given = "Douglas",
           family = "Phanstiel",
           role = c("aut")),
    person(given = "Michael",
           family = "Love",
           role = c("aut"))
           )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
URL: https://github.com/dozmorovlab/CTCF
BugReports: https://github.com/dozmorovlab/CTCF/issues
Suggests: 
    BiocStyle,
    rmarkdown,
    knitr,
    AnnotationHub,
    GenomicRanges,
    plyranges,
    sessioninfo
VignetteBuilder: knitr
biocViews: AnnotationData, AnnotationHub, FunctionalAnnotation, GenomicSequence