Package: baldur
Title: Bayesian Hierarchical Modeling for Label-Free Proteomics
Version: 0.0.4
Authors@R: 
    person("Philip", "Berg", , "pberg@live.se", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3772-6185"))
Description: Statistical decision in proteomics data using a
        hierarchical Bayesian model. There are two regression models
        for describing the mean-variance trend, a gamma regression or a
        latent gamma mixture regression. The regression model is then
        used as an Empirical Bayes estimator for the prior on the
        variance in a peptide. Further, it assumes that each
        measurement has an uncertainty (increased variance) associated
        with it that is also inferred. Finally, it tries to estimate
        the posterior distribution (by Hamiltonian Monte Carlo) for the
        differences in means for each peptide in the data. Once the
        posterior is inferred, it integrates the tails to estimate the
        probability of error from which a statistical decision can be
        made. See Berg and Popescu for details
        (<doi:10.1016/j.mcpro.2023.100658>).
License: MIT + file LICENSE
URL: https://github.com/PhilipBerg/baldur
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Biarch: true
Depends: R (>= 4.2.0)
Imports: dplyr (>= 1.0.9), magrittr (>= 2.0.3), methods, purrr (>=
        0.3.4), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>=
        2.26.0), rstantools (>= 2.2.0), stats, stringr (>= 1.0.4),
        tidyr (>= 1.2.0), rlang (>= 1.0.2), Rdpack (>= 2.4), multidplyr
        (>= 0.1.1), ggplot2 (>= 3.3.6), tibble (>= 3.1.7), viridisLite
        (>= 0.4.1), lifecycle
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>=
        2.26.0)
SystemRequirements: GNU make
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
RdMacros: Rdpack
BugReports: https://github.com/PhilipBerg/baldur/issues
Config/pak/sysreqs: cmake make libicu-dev
Repository: https://philipberg.r-universe.dev
Date/Publication: 2025-11-08 21:54:56 UTC
RemoteUrl: https://github.com/philipberg/baldur
RemoteRef: HEAD
RemoteSha: d28dd18c755c98b825ccf4f510504c4a660037ba
NeedsCompilation: yes
Packaged: 2026-10-04 09:44:26 UTC; root
Author: Philip Berg [aut, cre] (ORCID: <https://orcid.org/0000-0002-3772-6185>)
Maintainer: Philip Berg <pberg@live.se>