SWATH2stats

This is the released version of SWATH2stats; for the devel version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

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DOI: 10.18129/B9.bioc.SWATH2stats

Bioconductor version: Release (3.22)

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 "4.5") and enter:


if (!require("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")

SWATH2stats example script PDF R Script

SWATH2stats package Vignette PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software

Version 1.40.0

In Bioconductor since BioC 3.2 (R-3.2) (10 years)

License GPL-3

Depends R (>= 2.10.0)

Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods

System Requirements

URL https://peterblattmann.github.io/SWATH2stats/

Bug Reports https://github.com/peterblattmann/SWATH2stats

Suggests testthat, knitr, rmarkdown

Linking To

Enhances MSstats, PECA, aLFQ

Depends On Me

Imports Me

Suggests Me

Links To Me

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Package Archives

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

Source Package SWATH2stats_1.40.0.tar.gz

Windows Binary (x86_64) SWATH2stats_1.40.0.zip

macOS Binary (x86_64) SWATH2stats_1.40.0.tgz

macOS Binary (arm64) SWATH2stats_1.40.0.tgz

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/

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