sapFinder

DOI: 10.18129/B9.bioc.sapFinder    

A package for variant peptides detection and visualization in shotgun proteomics.

Bioconductor version: Release (3.6)

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

Author: Shaohang Xu, Bo Wen

Maintainer: Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("sapFinder")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sapFinder")

 

PDF	R Script	sapFinder Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 years)
License	GPL-2
Depends	R (>= 3.0.0), rTANDEM(>= 1.3.5)
Imports	pheatmap, Rcpp (>= 0.10.6), graphics, grDevices, stats, utils
LinkingTo	Rcpp
Suggests	RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	sapFinder_1.16.0.tar.gz
Windows Binary	sapFinder_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	sapFinder_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sapFinder
Package Short Url	http://bioconductor.org/packages/sapFinder/
Package Downloads Report	Download Stats