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ORFik:Open Reading Frames in Genomics
R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.
Maintained by Haakon Tjeldnes. Last updated 1 months ago.
immunooncologysoftwaresequencingriboseqrnaseqfunctionalgenomicscoveragealignmentdataimportcpp
33 stars 10.56 score 115 scripts 2 dependentsbioc
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.
Maintained by Vasily V. Grinev. Last updated 5 months ago.
technologystatisticalmethodsequencingrnaseqclassificationfeatureextractioncpp
1 stars 4.48 score