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 (3.11)

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 <mail at sebastiangibb.de>, Pavel Shliaha <pavels at bmb.sdu.dk>, Ole Jensen <jenseno at bmb.sdu.dk>, Nørregaard Gibb <mail at sebastiangibb.de>

Maintainer: Sebastian Gibb <mail at sebastiangibb.de>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("topdownr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.9.0
In Bioconductor since BioC 3.6 (R-3.4) (2 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 (>= 1.2.10), MSnbase(>= 2.3.10), ggplot2 (>= 2.2.1), mzR(>= 2.11.4)
LinkingTo
Suggests topdownrdata(>= 0.2), knitr, 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
Windows Binary
Mac OS X 10.11 (El Capitan)
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 https://bioconductor.org/packages/topdownr/
Package Downloads Report Download Stats

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