ORFhunteR

Predict open reading frames in nucleotide sequences


Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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")
The ORFhunteR package: User’s manual HTML R Script
Reference Manual PDF

Details

biocViews Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology
Version 1.12.0
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
See More
Suggests knitr, BiocStyle, rmarkdown
Linking To Rcpp
Enhances
Depends On Me
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Package Archives

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

Source Package ORFhunteR_1.12.0.tar.gz
Windows Binary (x86_64) ORFhunteR_1.12.0.zip
macOS Binary (x86_64) ORFhunteR_1.12.0.tgz
macOS Binary (arm64) ORFhunteR_1.12.0.tgz
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