SWATH2stats

DOI: 10.18129/B9.bioc.SWATH2stats  

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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	1.28.0
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 years)
License	GPL-3
Depends	R (>= 2.10.0)
Imports	data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
LinkingTo
Suggests	testthat, knitr, rmarkdown
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_1.28.0.tar.gz
Windows Binary	SWATH2stats_1.28.0.zip
macOS Binary (x86_64)	SWATH2stats_1.28.0.tgz
macOS Binary (arm64)	SWATH2stats_1.28.0.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/
Package Downloads Report	Download Stats