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
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:34:36 UTC
RemoteUrl: https://github.com/bioc/preciseTADhub
RemoteRef: HEAD
RemoteSha: da3b1bff4c527b5eebe3836eba174618500e3792
Packaged: 2026-10-10 10:43:03 UTC; root
Author: Spiro Stilianoudakis [aut],
  Mikhail Dozmorov [aut, cre]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>