DOI: 10.18129/B9.bioc.FScanR  

This is the development version of FScanR; for the stable release version, see FScanR.

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Bioconductor version: Development (3.19)

'FScanR' identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX homolog sequence alignment between targeted genomic/cDNA/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of 'FScanR' and should be in a tabular format with 14 columns. For BLASTX, the output parameter should be: -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe'. For diamond BLASTX, the output parameter should be: -outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe qframe.

Author: Xiao Chen [aut, cre]

Maintainer: Xiao Chen <seanchen607 at gmail.com>

Citation (from within R, enter citation("FScanR")):


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biocViews Alignment, Annotation, Software
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports stats
Suggests knitr, rmarkdown
BugReports https://github.com/seanchen607/FScanR/issues
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