The goal of Baldur is to shine light on your proteomics data. Baldur is a hierarchical Bayesian model that uses an empirical Bayes method to estimate hyperparamters for the variance and measurement specific uncertainty. It then estimates the posterior of the difference in means between different conditions for each peptide/protein/PTM. Finally, it integrates the posterior to estimate the probability of error.
You can install the development version of baldur from this github or
the stable version from CRAN. Importantly, you first need to follow the
instructions for installing rstan
https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started and make
sure that is working. Then you can install baldur accordingly:
For the stable release please install from CRAN:
install.packages('baldur')Or you can install the developmental version of baldur from this
github:
devtools::install_github('PhilipBerg/baldur', build_vignettes = T)Note that Ubuntu operating systems can require pandoc
https://pandoc.org/ to compile the vignettes.
For Windows, the developmental version of rstan is sometimes needed to
install baldur.
Please see the vignettes for examples
vignette('baldur_yeast_tutorial') and
vignette('baldur_ups_tutorial').
Berg, Philip, and George Popescu. “Baldur: Bayesian Hierarchical Modeling for Label-Free Proteomics with Gamma Regressing Mean-Variance Trends” Molecular & Cellular Proteomics (2023): 2023-12. https://doi.org/10.1016/j.mcpro.2023.100658