utr.annotation R package

This package can be used to annotate potential deleterious variants in the UTR regions for both human and mouse species. Given a CSV or VCF format variant file, utr.annotation provides information of each variant on whether and how it alters disrupts six known translational regulators including: upstream Open Reading Frames (uORFs), upstream Kozak sequences, polyA signals, the Kozak sequence at the annotated translation initiation site, start codon, and stop codon, conservation scores in the variant position, and whether and how it changes ribosome loading based on a model from empirical data.

The package has been tested on Linux and MacOS (Intel chip). If you are on Windows, getting conservation scores and ribosome loading prediction may not work, you could skip those two.

Input

Here is an example input file

Feature implementation

Here is a description of the key terms

UTR annotation results

Here is a description of the key annotation columns output from the UTR annotation.

Installation

Install dependencis

cran_pkgs <- c("parallel", "doParallel", "data.table", "readr", "stringr", "vcfR", "dplyr", "tidyr", "keras", "devtools", "reticulate")
bioc_pkgs <- c("biomaRt", "Biostrings", "AnnotationHub", "ensembldb")

for (pkg in cran_pkgs) {
  if (!(pkg %in% installed.packages())) {
    install.packages(pkg)
  }
}

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
}

for (pkg in bioc_pkgs) {
  if (!(pkg %in% installed.packages())) {
    BiocManager::install(pkg)
  }
}

# Install keras package for MRL prediction. 
library(keras)
# Install tensorflow backend
reticulate::install_miniconda()
keras::install_keras(version = "2.2.4", tensorflow = "1.14.0", method = "conda")

# install deep learning model data package
devtools::install_bitbucket("jdlabteam/mrl.dl.model")

Install utr.annotation package

# Install the release version from CRAN
install.packages("utr.annotation")

# Or install the latest version from Bitbucket
devtools::install_bitbucket("jdlabteam/utr.annotation")

Usage

Introduction to utr.annotation package

Citation

Y Liu, JD Dougherty. 2021. utR.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation. bioRxiv doi: 10.1101/2021.06.23.449510