DOI: 10.18129/B9.bioc.preciseTADhub    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see preciseTADhub.

Pre-trained random forest models obtained using preciseTAD

Bioconductor version: 3.13

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 for more detail on the model building strategy.

Author: Spiro Stilianoudakis [aut, cre], Mikhail Dozmorov [aut]

Maintainer: Spiro Stilianoudakis <stilianoudasc at>

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biocViews ExperimentData, ExperimentHub, Genome, PackageTypeData
Version 1.0.0
License MIT + file LICENSE
Depends R (>= 4.1)
Imports ExperimentHub
Suggests knitr, rmarkdown, BiocStyle, preciseTAD
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