sapFinder

DOI: 10.18129/B9.bioc.sapFinder    

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

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("sapFinder")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("sapFinder", version = "3.8")

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 MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 2.14 (R-3.1) (4.5 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_1.20.0.tar.gz
Windows Binary sapFinder_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) sapFinder_1.20.0.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 http://bioconductor.org/packages/sapFinder/
Package Downloads Report Download Stats

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