sapFinder

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("sapFinder")

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

Documentation

PDF R Script sapFinder Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization
Version 1.3.1
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-2
Depends R (>= 3.0.0), rTANDEM(>= 1.3.5)
Imports pheatmap, Rcpp (>= 0.10.6), graphics, grDevices, stats, utils
Suggests RUnit, BiocGenerics, BiocStyle
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source sapFinder_1.3.1.tar.gz
Windows Binary sapFinder_1.3.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) sapFinder_1.3.1.tgz
Mac OS X 10.9 (Mavericks) sapFinder_1.3.1.tgz
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