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SWATH2stats

This is the development version of SWATH2stats; for the stable release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: Development (3.18)

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 <peter_blattmann at bluewin.ch>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software
Version 1.31.1
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
Linking To
Suggests testthat, knitr, rmarkdown
System Requirements
Enhances MSstats, PECA, aLFQ
URL https://peterblattmann.github.io/SWATH2stats/
Bug Reports https://github.com/peterblattmann/SWATH2stats
See More
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_1.31.1.tar.gz
Windows Binary SWATH2stats_1.31.1.zip (64-bit only)
macOS Binary (x86_64) SWATH2stats_1.31.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SWATH2stats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SWATH2stats
Bioc Package Browser https://code.bioconductor.org/browse/SWATH2stats/
Package Short Url https://bioconductor.org/packages/SWATH2stats/
Package Downloads Report Download Stats