baldur-package | The 'baldur' package. |
baldur | The 'baldur' package. |
calculate_mean_sd_trends | Calculate the Mean-Variance trend |
coef.lgmr | Fit Latent Gamma Mixture Regression |
empirical_bayes | Baldur's empirical Bayes Prior For The Mean In Conditions |
estimate_beta | Estimate Gamma hyperparameters for sigma |
estimate_beta.glm | Estimate Gamma hyperparameters for sigma |
estimate_beta.lgmr | Estimate Gamma hyperparameters for sigma |
estimate_gamma_hyperparameters | Estimate Gamma hyperparameters for sigma |
estimate_gamma_hyperparameters.glm | Estimate Gamma hyperparameters for sigma |
estimate_gamma_hyperparameters.lgmr | Estimate Gamma hyperparameters for sigma |
estimate_uncertainty | Estimate measurement uncertainty |
estimate_uncertainty.glm | Estimate measurement uncertainty |
estimate_uncertainty.lgmr | Estimate measurement uncertainty |
fit_gamma_regression | Function for Fitting the Mean-Variance Gamma Regression Models |
fit_lgmr | Fit Latent Gamma Mixture Regression |
infer_data_and_decision_model | Sample the Posterior of the data and decision model and generate point estimates |
lgmr_model | Latent Gamma Regression Model |
lgmr_plotting | Visualization of LGMR models |
plot_gamma | Function for plotting the gamma regression for the mean-variance trend |
plot_gamma_regression | Function for plotting the mean-variance gamma regressions |
plot_lgmr_regression | Visualization of LGMR models |
plot_regression_field | Visualization of LGMR models |
plot_sa | Plot the trend between the log fold-change and sigma, coloring significant hits |
plot_volcano | Plot the -log10(err) against the log fold-change |
print.lgmr | Fit Latent Gamma Mixture Regression |
psrn | Normalize data to a pseudo-reference |
ups | Spiked-in data set of peptides |
weakly_informative | Baldur's weakly informative prior for the mean in conditions |
yeast | Spiked-in data set of reversibly oxidized cysteines |