Package: ORFhunteR 1.15.0
Vasily V. Grinev
ORFhunteR: Predict open reading frames in nucleotide sequences
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.
Authors:
ORFhunteR_1.15.0.tar.gz
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ORFhunteR.pdf |ORFhunteR.html✨
ORFhunteR/json (API)
| # Install 'ORFhunteR' in R: |
| install.packages('ORFhunteR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rfctbio-bsu/orfhunter/issues
On BioConductor:ORFhunteR-1.15.0(bioc 3.21)ORFhunteR-1.14.0(bioc 3.20)
technologystatisticalmethodsequencingrnaseqclassificationfeatureextraction
Last updated 2 months agofrom:7fcb3eee59. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 20 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 20 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 20 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 20 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 20 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 20 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 20 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 20 2024 |
Exports:annotateORFsclassifyORFsCandidatescodonStartStopfindORFsfindPTCsgetSeqORFsloadTrExperpredictORFtranslateORFsvectorizeORFs
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg38clicodetoolscpp11crayoncurldata.tableDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslPeptidesR6randomForestRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate open reading frames | annotateORFs |
| Classify the pseudo and true ORF candidates derived from RNA molecules | classifyORFsCandidates |
| Identify all potential start and stop codons in a nucleotide sequence | codonStartStop |
| Identify all variants of open reading frames in a nucleotide sequence | findORFs |
| Identify the premature termination codons in nucleotide sequences | findPTCs |
| Extract the sequences of identified open reading frames | getSeqORFs |
| Load a set of transcripts | loadTrExper |
| Predict the true ORFs in mRNA molecules | predictORF |
| Translate open reading frames to proteins | translateORFs |
| Vectorize the ORF(-s) sequence(-s) to sequence features | vectorizeORFs |
