topdownr
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see topdownr.
Investigation of Fragmentation Conditions in Top-Down Proteomics
Bioconductor version: 3.19
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>
citation("topdownr")):
Installation
To install this package, start R (version "4.4") 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")| Data Generation for topdownr | HTML | R Script |
| Fragmentation Analysis with topdownr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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), PSMatch(>= 1.6.0), ggplot2 (>= 2.2.1), mzR(>= 2.27.5) |
| System Requirements | |
| URL | https://github.com/sgibb/topdownr/ |
| Bug Reports | https://github.com/sgibb/topdownr/issues/ |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | topdownr_1.26.0.tar.gz |
| Windows Binary (x86_64) | topdownr_1.26.0.zip |
| macOS Binary (x86_64) | topdownr_1.26.0.tgz |
| macOS Binary (arm64) | topdownr_1.26.0.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 3.19 | Source Archive |