preciseTADhub
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see preciseTADhub.
Pre-trained random forest models obtained using preciseTAD
Bioconductor version: 3.19
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("preciseTADhub")):
Installation
To install this package, start R (version "4.4") 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 | ||
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Genome, PackageTypeData |
| Version | 1.12.0 |
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |