topdownr
Investigation of Fragmentation Conditions in Top-Down Proteomics
Bioconductor version: 3.24 · Package version: 1.35.1
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("topdownr")Details
| Maintainer | Sebastian Gibb <mail@sebastiangibb.de> |
| Author | Sebastian Gibb [aut, cre] (ORCID: <https://orcid.org/0000-0001-7406-4443>), Pavel Shliaha [aut] (ORCID: <https://orcid.org/0000-0003-3092-0724>), Ole Nørregaard Jensen [aut] (ORCID: <https://orcid.org/0000-0003-1862-8528>) |
| License | GPL (>= 3) |
| URL | https://codeberg.org/sgibb/topdownr/ |
| Bug Reports | https://codeberg.org/sgibb/topdownr/issues/ |
| Downloads rank | 540 |
| Source branch | devel |
| biocViews | Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software |
Documentation
Download
Follow the 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 (arm64) | topdownr_1.35.1.tgz |
| macOS binary (x86_64) | topdownr_1.35.1.tgz |
Dependencies
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)
Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2
Reverse dependencies
Depends On Me (1): topdownrdata