SWATH2stats

DOI: 10.18129/B9.bioc.SWATH2stats    

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: Release (3.12)

This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

Author: Peter Blattmann [aut, cre] Moritz Heusel [aut] Ruedi Aebersold [aut]

Maintainer: Peter Blattmann <blattmann at imsb.biol.ethz.ch>

Citation (from within R, enter citation("SWATH2stats")):

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("SWATH2stats")

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("SWATH2stats")

 

PDF R Script SWATH2stats example script
PDF R Script SWATH2stats package Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software
Version 1.20.0
In Bioconductor since BioC 3.2 (R-3.2) (5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
LinkingTo
Suggests testthat, knitr
SystemRequirements
Enhances MSstats, PECA, aLFQ
URL https://peterblattmann.github.io/SWATH2stats/
BugReports https://github.com/peterblattmann/SWATH2stats
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 SWATH2stats_1.20.0.tar.gz
Windows Binary SWATH2stats_1.20.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) SWATH2stats_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SWATH2stats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SWATH2stats
Package Short Url https://bioconductor.org/packages/SWATH2stats/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: