ORFhunteR

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

Predict open reading frames in nucleotide sequences

Bioconductor version: Development (3.21)

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] (ORCID: ), Mikalai M. Yatskou [aut], Victor V. Skakun [aut], Maryna Chepeleva [aut] (ORCID: ), Petr V. Nazarov [aut] (ORCID: )

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

Citation (from within R, enter citation("ORFhunteR")):

Installation

To install this package, start R (version "4.5") and enter:


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

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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology
Version	1.15.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	MIT License
Depends	Biostrings, rtracklayer, Peptides
Imports	Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics
System Requirements
URL
Bug Reports	https://github.com/rfctbio-bsu/ORFhunteR/issues

Suggests	knitr, BiocStyle, rmarkdown
Linking To	Rcpp
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	ORFhunteR_1.15.0.tar.gz
Windows Binary (x86_64)	ORFhunteR_1.15.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ORFhunteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ORFhunteR
Bioc Package Browser	https://code.bioconductor.org/browse/ORFhunteR/
Package Short Url	https://bioconductor.org/packages/ORFhunteR/
Package Downloads Report	Download Stats