Introduction | Installation | The data | A well-defined theoretical example | Preparing for bandle analysis | Fitting Gaussian processes | Setting the prior on the weights | Running the bandle function | Analysing bandle output | Assesing the model for convergence | Removing unconverged chains | Populating a bandleres object | Predicting the subcellular location | Thresholding on protein allocations | Distribution on allocations | Proteins assigned to one main location | Proteins with uncertainty | Differential localisation probability | Visualising differential localisation | Additional analysis | Estimating uncertainty in differential localisation | The bootstrapdiffLocprob function | The binomDiffLoc function | Obtaining probability estimates | The expected false discovery rate | Description of bandle parameters | Session information | References

Introduction | The data | Spatialtemporal proteomic profiling of a THP-1 cell line | Preparing the data | Preparing the bandle input parameters | Fitting Gaussian processes | Setting the prior on the weights | Running bandle | Processing and analysing the bandle results | Assessing convergence | Removing unconverged chains | Running bandleProcess and bandleSummary | Predicting subcellular location | Thresholding on the posterior probability | Distribution on allocations | Proteins assigned to one main location | Proteins with uncertainty | Differential localisation | Visualising differential localisation | Alluvial plots | Protein profiles | Session information | References

Introduction | packages | Data | Visualisation | Examining missing values | Empirical vs Theoretical errors | Intensity based outlier detection | Retention time analysis | Monotonicity statistics | Ion Mobility Time analysis | Charge state correlation | Using replicates to determine outliers and variability | Using sequence overlap information are uptake values compatible | Comparison of Spectra