ORFhunteR
Predict open reading frames in nucleotide sequences
Bioconductor version: Release (3.20)
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("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 |
Details
| biocViews | Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology |
| Version | 1.14.0 |
| 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 | |
| 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | ORFhunteR_1.14.0.zip |
| macOS Binary (x86_64) | ORFhunteR_1.14.0.tgz |
| macOS Binary (arm64) | ORFhunteR_1.14.0.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 |