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topdownr

Investigation of Fragmentation Conditions in Top-Down Proteomics


Bioconductor version: Release (3.18)

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 sebastiangibb.de>

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

Installation

To install this package, start R (version "4.3") 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")
Data Generation for topdownr HTML R Script
Fragmentation Analysis with topdownr HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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(>= 2.3.10), 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
Suggests topdownrdata(>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2
Linking To
Enhances
Depends On Me topdownrdata
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 topdownr_1.24.0.tar.gz
Windows Binary topdownr_1.24.0.zip
macOS Binary (x86_64) topdownr_1.24.0.tgz
macOS Binary (arm64) topdownr_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/topdownr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/topdownr
Bioc Package Browser https://code.bioconductor.org/browse/topdownr/
Package Short Url https://bioconductor.org/packages/topdownr/
Package Downloads Report Download Stats