sapFinder

DOI: 10.18129/B9.bioc.sapFinder    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see sapFinder.

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

Bioconductor version: 3.9

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 (version "3.6") and enter:

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

BiocManager::install("sapFinder")

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("sapFinder")

 

PDF	R Script	sapFinder Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization
Version	1.22.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 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
Links To Me
Build Report

Package Archives

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

Source Package	sapFinder_1.22.0.tar.gz
Windows Binary	sapFinder_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	sapFinder_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sapFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sapFinder
Package Short Url	https://bioconductor.org/packages/sapFinder/
Package Downloads Report	Download Stats