preciseTADhub

DOI: 10.18129/B9.bioc.preciseTADhub    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see preciseTADhub.

Pre-trained random forest models obtained using preciseTAD

Bioconductor version: 3.15

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.

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

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("preciseTADhub")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("preciseTADhub")

 

HTML	R Script	preciseTADhub
PDF		Reference Manual
Text		LICENSE

Details

biocViews	ExperimentData, ExperimentHub, Genome, PackageTypeData
Version	1.4.0
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	ExperimentHub
LinkingTo
Suggests	knitr, rmarkdown, markdown, BiocStyle, preciseTAD
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/preciseTADhub
BugReports	https://github.com/dozmorovlab/preciseTADhub/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	preciseTADhub_1.4.0.tar.gz
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/preciseTADhub
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/preciseTADhub
Package Short Url	https://bioconductor.org/packages/preciseTADhub/
Package Downloads Report	Download Stats