sapFinder

DOI: 10.18129/B9.bioc.sapFinder    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 "4.0") 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 1.28.0
In Bioconductor since BioC 2.14 (R-3.1) (7 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_1.28.0.tar.gz
Windows Binary sapFinder_1.28.0.zip (64-bit only)
macOS 10.13 (High Sierra)
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

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