topdownr

DOI: 10.18129/B9.bioc.topdownr    

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Release (3.6)

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] (0000-0001-7406-4443), Pavel Shliaha [aut], Ole Nørregaard Jensen [aut]

Maintainer: Sebastian Gibb <mail at sebastiangibb.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("topdownr")

Documentation

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	1.0.0
License	GPL (>= 3)
Depends	R (>= 3.4), methods, BiocGenerics(>= 0.20.0), Biostrings(>= 2.42.1), S4Vectors(>= 0.12.2)
Imports	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
Build Report

Package Archives

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

Source Package	topdownr_1.0.0.tar.gz
Windows Binary	topdownr_1.0.0.zip
Mac OS X 10.11 (El Capitan)	topdownr_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/topdownr
Package Short Url	http://bioconductor.org/packages/topdownr/
Package Downloads Report	Download Stats