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 (3.24)
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("SWATH2stats")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| SWATH2stats package Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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 |
See More
| 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_1.43.0.tar.gz |
| Windows Binary (x86_64) | SWATH2stats_1.43.0.zip |
| macOS Binary (big-sur-x86_64) | SWATH2stats_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | SWATH2stats_1.43.0.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 |