DOI: 10.18129/B9.bioc.topdownr    

This is the development version of topdownr; for the stable release version, see topdownr.

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Development (3.11)

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 <mail at>, Pavel Shliaha <pavels at>, Ole Jensen <jenseno at>, Nørregaard Gibb <mail at>

Maintainer: Sebastian Gibb <mail at>

Citation (from within R, enter citation("topdownr")):


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biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.9.0
In Bioconductor since BioC 3.6 (R-3.4) (2 years)
License GPL (>= 3)
Depends R (>= 3.5), 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, xml2
Depends On Me topdownrdata
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