ORFhunteR

DOI: 10.18129/B9.bioc.ORFhunteR    

This is the development version of ORFhunteR; to use it, please install the devel version of Bioconductor.

Predict open reading frames in nucleotide sequences

Bioconductor version: Development (3.13)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology
Version 0.99.11
In Bioconductor since BioC 3.13 (R-4.1)
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
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ORFhunteR_0.99.11.tar.gz
Windows Binary ORFhunteR_0.99.11.zip (32- & 64-bit)
macOS 10.13 (High Sierra) ORFhunteR_0.99.11.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

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