DOI: 10.18129/B9.bioc.ORFhunteR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ORFhunteR.

Predict open reading frames in nucleotide sequences

Bioconductor version: 3.16

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>

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biocViews Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
BugReports https://github.com/rfctbio-bsu/ORFhunteR/issues
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Source Package ORFhunteR_1.6.0.tar.gz
Windows Binary ORFhunteR_1.6.0.zip
macOS Binary (x86_64) ORFhunteR_1.6.0.tgz
macOS Binary (arm64) ORFhunteR_1.6.0.tgz
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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/
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