topdownr

This is the development version of topdownr; for the stable release version, see topdownr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-7406-4443 , Pavel Shliaha [aut] ORCID: 0000-0003-3092-0724 , Ole Nørregaard Jensen [aut] ORCID: 0000-0003-1862-8528

Maintainer: Sebastian Gibb <mail at sebastiangibb.de>

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

Sebastian Gibb, Pavel Shliaha, Ole Nørregaard Jensen. topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics. doi:10.18129/B9.bioc.topdownr, R package version 1.35.1, https://bioconductor.org/packages/topdownr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version	1.35.1
In Bioconductor since	BioC 3.6 (R-3.4) (9 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, IRanges, Matrix (>= 1.4-2), MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 3.0.0), mzR (>= 2.27.5)
System Requirements
URL	https://codeberg.org/sgibb/topdownr/
Bug Reports	https://codeberg.org/sgibb/topdownr/issues/

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, r-universe

Package Archives

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

Source Package	topdownr_1.35.1.tar.gz
Windows Binary (x86_64)	topdownr_1.35.1.zip
macOS Binary (big-sur-x86_64)	topdownr_1.35.1.tgz
macOS Binary (sonoma-arm64)	topdownr_1.35.1.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	https://bioconductor.org/packages/topdownr/
Package Downloads Report	Download Stats