bandle                  Differential localisation experiments using the
                        bandle method
bandle_get_outliers     Number of outliers at each iteration of MCMC
bandle-package          An R package for the Bayesian analysis of
                        differential subcellular localisation
                        experiments
bandleChains-class      Infrastructure to to store and process MCMC
                        results
bandlePredict           Make predictions from a bandle analysis
bandleProcess           process bandle results
besselK_boost           bessel function of the second kind from boost
                        library
calculateGelman         Calculate the Gelman and Rubin diagnostic for
                        bandle output
diffLocalisationProb    Compute differential localisation probabilities
                        from ms-based experiments using the bandle
                        method
EFDR                    Compute the expected False Discovery Rate
fitGP                   Fit a Gaussian process to spatial proteomics
                        data
gpParams-class          Container for GP results
gradientGP              Compute GP gradient
kldirpg                 Computes the Kullback-Leibler divergence
                        between Polya-Gamma and Dirichlet priors
mcmc_plot_probs         Generate a violin plot showing the probabilitiy
                        of protein localisation to different organelles
meanOrganelle           Computes Organelle means and variances using
                        markers
plotConvergence         Generates a histogram of ranks (a rank plot)
                        for convergence
plotOutliers            Generate trace and density plots for all chains
plotTable               Generate a table of differential localisations
plotTranslocations      Plot changes in localisation between two
                        conditions/datasets
proteinAllocation       sample allocations, probabilities and compute
                        loglikilihoods
robustMahalanobis       robust Mahalanobis distance
sim_dynamic             Generate a dynamic spatial proteomics
                        experiment
spatial2D               Generate a PCA plot with smoothed probability
                        contours
StatStratum             inherits StatSratum
