SWATH2stats

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: 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")

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	1.32.1
In Bioconductor since	BioC 3.2 (R-3.2) (8.5 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
Build Report	Build Report

Package Archives

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

Source Package	SWATH2stats_1.32.1.tar.gz
Windows Binary	SWATH2stats_1.32.1.zip
macOS Binary (x86_64)	SWATH2stats_1.32.1.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
Old Source Packages for BioC 3.18	Source Archive