preciseTADhub

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see preciseTADhub.

Pre-trained random forest models obtained using preciseTAD


Bioconductor version: 3.17

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>

Citation (from within R, enter citation("preciseTADhub")):

Installation

To install this package, start R (version "4.3") 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")
preciseTADhub HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews ExperimentData, ExperimentHub, Genome, PackageTypeData
Version 1.8.0
License MIT + file LICENSE
Depends R (>= 4.1)
Imports ExperimentHub
System Requirements
URL https://github.com/dozmorovlab/preciseTADhub
Bug Reports https://github.com/dozmorovlab/preciseTADhub/issues
See More
Suggests knitr, rmarkdown, markdown, BiocStyle, preciseTAD
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package preciseTADhub_1.8.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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