ORFhunteR

DOI: 10.18129/B9.bioc.ORFhunteR    

Predict open reading frames in nucleotide sequences

Bioconductor version: Release (3.15)

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.

Author: Vasily V. Grinev [aut, cre] , Mikalai M. Yatskou [aut], Victor V. Skakun [aut], Maryna Chepeleva [aut], Petr V. Nazarov [aut]

Maintainer: Vasily V. Grinev <grinev_vv at bsu.by>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("ORFhunteR")

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("ORFhunteR")

 

HTML	R Script	The ORFhunteR package: User’s manual
PDF		Reference Manual

Details

biocViews	Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	Artistic-2.0
Depends	Biostrings, rtracklayer, Peptides
Imports	Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics
LinkingTo	Rcpp
Suggests	knitr, BiocStyle, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/rfctbio-bsu/ORFhunteR/issues
Depends On Me
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Build Report

Package Archives

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

Source Package	ORFhunteR_1.4.0.tar.gz
Windows Binary	ORFhunteR_1.4.0.zip
macOS Binary (x86_64)	ORFhunteR_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ORFhunteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ORFhunteR
Package Short Url	https://bioconductor.org/packages/ORFhunteR/
Package Downloads Report	Download Stats