preciseTAD
preciseTAD: A machine learning framework for precise TAD boundary prediction
Bioconductor version: Release (3.20)
preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.
Author: Spiro Stilianoudakis [aut], Mikhail Dozmorov [aut, cre]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
citation("preciseTAD")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("preciseTAD")
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("preciseTAD")| preciseTAD | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, FeatureExtraction, FunctionalGenomics, HiC, Sequencing, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH |
| System Requirements | |
| URL | https://github.com/dozmorovlab/preciseTAD |
| Bug Reports | https://github.com/dozmorovlab/preciseTAD/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | preciseTADhub |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | preciseTAD_1.16.0.tar.gz |
| Windows Binary (x86_64) | preciseTAD_1.16.0.zip |
| macOS Binary (x86_64) | preciseTAD_1.16.0.tgz |
| macOS Binary (arm64) | preciseTAD_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/preciseTAD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/preciseTAD |
| Bioc Package Browser | https://code.bioconductor.org/browse/preciseTAD/ |
| Package Short Url | https://bioconductor.org/packages/preciseTAD/ |
| Package Downloads Report | Download Stats |