sapFinder

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see sapFinder.

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


Bioconductor version: 3.10

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 "3.6") and enter:


if (!require("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")
sapFinder Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization
Version 1.24.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-2
Depends R (>= 3.0.0), rTANDEM(>= 1.3.5)
Imports pheatmap, Rcpp (>= 0.10.6), graphics, grDevices, stats, utils
System Requirements
URL
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Suggests RUnit, BiocGenerics, BiocStyle
Linking To Rcpp
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package sapFinder_1.24.0.tar.gz
Windows Binary sapFinder_1.24.0.zip
Mac OS X 10.11 (El Capitan) sapFinder_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sapFinder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sapFinder
Bioc Package Browser https://code.bioconductor.org/browse/sapFinder/
Package Short Url https://bioconductor.org/packages/sapFinder/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive