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 exploiting gamma dependent mean-variance trends.” bioRxiv (2023): 2023-05. https://doi.org/10.1101/2023.05.11.540411