topdownr

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 (3.9)

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] (<https://orcid.org/0000-0001-7406-4443>), Pavel Shliaha [aut] (<https://orcid.org/0000-0003-3092-0724>), Ole Nørregaard Jensen [aut] (<https://orcid.org/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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("topdownr", version = "3.9")

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, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.5.1
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)
LinkingTo
Suggests topdownrdata(>= 0.2), knitr, ranger, testthat, BiocStyle
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_1.5.1.tar.gz
Windows Binary topdownr_1.5.1.zip
Mac OS X 10.11 (El Capitan) topdownr_1.5.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/topdownr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/topdownr
Package Short Url http://bioconductor.org/packages/topdownr/
Package Downloads Report Download Stats

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