Package: baldur
Title: Bayesian Hierarchical Modeling for Label-Free Proteomics
Version: 0.0.3
Authors@R: 
    person("Philip", "Berg", , "pb1015@msstate.edu", 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:10.1101/2023.05.11.540411>).
License: MIT + file LICENSE
URL: https://github.com/PhilipBerg/baldur
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.2.3
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
NeedsCompilation: yes
Packaged: 2023-09-12 15:21:02 UTC; Pberg
Author: Philip Berg [aut, cre] (<https://orcid.org/0000-0002-3772-6185>)
Maintainer: Philip Berg <pb1015@msstate.edu>
Repository: CRAN
Date/Publication: 2023-09-18 08:50:05 UTC
Built: R 4.5.0; aarch64-apple-darwin20; 2025-01-22 06:57:09 UTC; unix
Archs: baldur.so.dSYM
