SWATH2stats (version 1.2.3)

SWATH2stats-package: SWATH2stats

Description

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 assessment.

Details

Package:

SWATH2stats

Type:

Package

Version:

1.2.3

Date:

2016-05-22

License:

GPLv3

References

Blattmann P, Heusel M, Aebersold R. SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools. PLoS ONE 11(4): e0153160 (2016). doi: 10.1371/journal.pone.0153160.

Rost HL, Rosenberger G, Navarro P, Gillet L, Miladinovic SM, Schubert OT, Wolski W, Collins BC, Malmstrom J, Malmstrom L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841.

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305.

Rosenberger G, Ludwig C, Rost HL, Aebersold R, Malmstrom L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200.

See Also

aLFQ, MSstats,