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Bioconductor - topdownr

topdownr

This is the released version of topdownr; for the devel version, see topdownr.

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-7406-4443 , Pavel Shliaha [aut] ORCID: 0000-0003-3092-0724 , Ole Nørregaard Jensen [aut] ORCID: 0000-0003-1862-8528

Maintainer: Sebastian Gibb <mail at sebastiangibb.de>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("topdownr")

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("topdownr")
Details biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software Version 1.30.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 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 (>= 1.4-2), MSnbase(>= 2.33.5), PSMatch(>= 1.11.4), ggplot2 (>= 2.2.1), mzR(>= 2.27.5) System Requirements URL https://github.com/sgibb/topdownr/ Bug Reports https://github.com/sgibb/topdownr/issues/ See More Package Archives

Follow Installation instructions to use this package in your R session.

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