FScanR

DOI: 10.18129/B9.bioc.FScanR  

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Bioconductor version: Release (3.16)

'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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FScanR")

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("FScanR")

 

HTML	R Script	FScanR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	stats
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/seanchen607/FScanR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	FScanR_1.8.0.tar.gz
Windows Binary	FScanR_1.8.0.zip
macOS Binary (x86_64)	FScanR_1.8.0.tgz
macOS Binary (arm64)	FScanR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FScanR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FScanR
Bioc Package Browser	https://code.bioconductor.org/browse/FScanR/
Package Short Url	https://bioconductor.org/packages/FScanR/
Package Downloads Report	Download Stats