biomasslmb is an R package which provide functions to pipe together proteomics data analysis pipelines using QFeatures for data generated by the Biological Mass Spectrometry and Proteomics Facility at the MRC Laboratory of Molecular Biology.
Alongside the general purpose functions for routine proteomics data analyses, this package also provides some more esoteric and/or opinionated functionality for bespoke proteomics data analysis.
Much of the initial code is a re-working of camprotR which was co-developed by Charlotte Dawson (https://github.com/csdaw) and myself (https://github.com/tomsmithCGAT) and was designed to work with MSnbase. Hence I’ve reworked the code here as a separate package to work with QFeatures to simplify issues with backward compatibility. Thank you to Charlotte for any of the code lifted from camprotR for which I had no part in writing!
Installation
You can install the development version of biomasslmb like so:
remotes::install_github("lmb-mass-spec-compbio/biomasslmb", dependencies = TRUE)Examples
See the vignettes for examples how to use the package. The vignettes are also available via the ‘articles’ tab here.