baldur
Bayesian Hierarchical Modeling for Label-Free Proteomics
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>).
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (17 non-OK)
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dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
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for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 95.4Mb
sub-directories of 1Mb or more:
data 1.2Mb
libs 93.5Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 97.4Mb
sub-directories of 1Mb or more:
data 1.2Mb
libs 95.4Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.1Mb
libs 3.4Mb
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Check History
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
installed package size
installed size is 95.4Mb
sub-directories of 1Mb or more:
data 1.2Mb
libs 93.5Mb
installed package size
installed size is 97.4Mb
sub-directories of 1Mb or more:
data 1.2Mb
libs 95.4Mb
installed package size
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.1Mb
libs 3.4Mb