Package: TOP
Title: Predict transcription factor occupancy using DNase- or ATAC-seq
        data
Version: 1.0.0
Authors@R: c(
  person("Kaixuan", "Luo", role = c("aut", "cre"), email = "kevinlkx@gmail.com"),
  person("Jianling", "Zhong", role = "aut", email = "jianlingzh@gmail.com"),
  person("Alex", "Hartemink", role = c("aut", "cph"), email = "amink@cs.duke.edu"))
Description: Transcription factor (TF) occupancy profiler (TOP) 
    predicts quantitative TF occupancy at candidate TF motif locations 
    across cell types or conditions.
    It is a Bayesian hierarchical model trained using quantitative 
    DNase- or ATAC-seq and ChIP-seq data 
    from many TFs and cell types (from ENCODE data).
    TOP learns both TF- and cell type- specific parameters as well 
    as TF-generic parameters jointly for TFs and cell types from existing 
    DNase-/ATAC-seq and ChIP-seq data. 
    Once trained, it could predict quantitative TF occupancy or 
    TF binding probability for TFs across cell types or conditions 
    using DNase- or ATAC- seq data
    without requring new ChIP data.
URL: https://github.com/HarteminkLab/TOP
BugReports: https://github.com/HarteminkLab/TOP/issues
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Depends: R (>= 3.5.0)
Imports: GenomicRanges, Rsamtools, data.table, R.utils, doParallel,
        foreach, ggplot2
Suggests: R2jags, GenomicAlignments, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-04-28 03:39:15 UTC; kaixuanluo
Author: Kaixuan Luo [aut, cre],
  Jianling Zhong [aut],
  Alex Hartemink [aut, cph]
Maintainer: Kaixuan Luo <kevinlkx@gmail.com>
