topdownr

DOI: 10.18129/B9.bioc.topdownr  

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Release (3.17)

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>

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")

 

HTML	R Script	Data Generation for topdownr
HTML	R Script	Fragmentation Analysis with topdownr
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version	1.22.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 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)
LinkingTo
Suggests	topdownrdata(>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2
SystemRequirements
Enhances
URL	https://github.com/sgibb/topdownr/
BugReports	https://github.com/sgibb/topdownr/issues/
Depends On Me	topdownrdata
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	topdownr_1.22.0.tar.gz
Windows Binary	topdownr_1.22.0.zip
macOS Binary (x86_64)	topdownr_1.22.0.tgz
macOS Binary (arm64)	topdownr_1.22.0.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
Old Source Packages for BioC 3.17	Source Archive