DOI: 10.18129/B9.bioc.topdownr    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see topdownr.

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: 3.8

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Author: Sebastian Gibb [aut, cre] , Pavel Shliaha [aut] , Ole Nørregaard Jensen [aut]

Maintainer: Sebastian Gibb <mail at>

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biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.4.1
In Bioconductor since BioC 3.6 (R-3.4) (1.5 years)
License GPL (>= 3)
Depends R (>= 3.4), methods, BiocGenerics(>= 0.20.0), ProtGenerics(>= 1.10.0), Biostrings(>= 2.42.1), S4Vectors(>= 0.12.2)
Imports grDevices, stats, tools, utils, Biobase, Matrix (>= 1.2.10), MSnbase(>= 2.3.10), ggplot2 (>= 2.2.1), mzR(>= 2.11.4)
Suggests topdownrdata(>= 0.2), knitr, ranger, testthat, BiocStyle
Depends On Me topdownrdata
Imports Me
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