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preciseTADhub

This is the development version of preciseTADhub; for the stable release version, see preciseTADhub.

Pre-trained random forest models obtained using preciseTAD


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.13.0
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
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Package Archives

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

Source Package preciseTADhub_1.13.0.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/
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