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FScanR

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output


Bioconductor version: Release (3.18)

'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")):

Installation

To install this package, start R (version "4.3") 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

Reference Manual PDF

Details

biocViews Alignment, Annotation, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports stats
System Requirements
URL
Bug Reports https://github.com/seanchen607/FScanR/issues
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Package Archives

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

Source Package
Windows Binary FScanR_1.12.0.zip (64-bit only)
macOS Binary (x86_64) FScanR_1.12.0.tgz
macOS Binary (arm64) FScanR_1.12.0.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/
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