FScanR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FScanR.
Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
Bioconductor version: 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("FScanR")):
Installation
To install this package, start R (version "4.4") 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 |
Details
| biocViews | Alignment, Annotation, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 | |
| Windows Binary (x86_64) | FScanR_1.14.0.zip |
| macOS Binary (x86_64) | FScanR_1.14.0.tgz |
| macOS Binary (arm64) | FScanR_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FScanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FScanR |
| Package Short Url | https://bioconductor.org/packages/FScanR/ |
| Package Downloads Report | Download Stats |