Registration and Call for Abstracts Open for Bioc2024

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
FScanR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Annotation, Software
Version 1.13.0
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
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package FScanR_1.13.0.tar.gz
Windows Binary FScanR_1.13.1.zip (64-bit only)
macOS Binary (x86_64) FScanR_1.13.1.tgz
macOS Binary (arm64) FScanR_1.13.0.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