Package: preciseTADhub
Type: Package
Title: Pre-trained random forest models obtained using preciseTAD
Version: 1.21.0
Authors@R: c(
    person("Spiro", "Stilianoudakis", 
        email = "stilianoudasc@vcu.edu", 
        role = c("aut")),
    person("Mikhail", "Dozmorov", 
        email = "mikhail.dozmorov@gmail.com", 
        role = c("aut", "cre")))
Description: An experimentdata package to supplement the preciseTAD package 
    containing pre-trained models and the variable importances of each genomic 
    annotation used to build the model parsed into list objects and available in
    ExperimentHub. In total, preciseTADhub provides access to n=84 random forest
    classification models optimized to predict TAD/chromatin loop boundary 
    regions and stored as .RDS files. The value, n, comes from the fact that 
    we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries 
    {Arrowhead, Peakachu}, and c=21 autosomal chromosomes 
    {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself
    a two-item list containing: (1) the model object, and (2) the variable 
    importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary 
    regions. Each model is trained via a "holdout" strategy, in which data from 
    chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build
    the model and the ith chromosome was reserved for testing. See 
    https://doi.org/10.1101/2020.09.03.282186 for more detail on the model 
    building strategy.
License: MIT + file LICENSE
Depends: R (>= 4.1)
Encoding: UTF-8
Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD
Imports: ExperimentHub
VignetteBuilder: knitr
biocViews: ExperimentData, PackageTypeData, ExperimentHub, Genome
NeedsCompilation: no
RoxygenNote: 7.1.1
BugReports: https://github.com/dozmorovlab/preciseTADhub/issues
URL: https://github.com/dozmorovlab/preciseTADhub
git_url: https://git.bioconductor.org/packages/preciseTADhub
git_branch: devel
git_last_commit: da3b1bf
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-04-30
Packaged: 2026-04-30 15:54:06 UTC; biocbuild
Author: Spiro Stilianoudakis [aut],
  Mikhail Dozmorov [aut, cre]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
