What is monitOS? | Core parameters | Installation | Scenario 1 — Standard trial: Follicular Lymphoma | Clinical context | Interpreting the output | Scenario 2 — Edge case: CLL Maintenance with Unequal Randomisation | Key observations for the edge case | Quick reference

Try monitOS in your browser | About Shinylive | Local Shiny App

Introduction | Example use-case: Dual combination trial with historical information | Setting up the trial design | Drug info | Dose info | Initializing a blrm_trial | Specifying the prior and fitting the model | Summary of prior specification | Summary of posterior | Posterior accuracy of EWOC estimation | Posterior predictive summaries | Updating the model with new data | Data scenarios | Continuation of example: Using concurrent data | References | Session Info

Introduction | Application background | Historical data | Derivation of MAP priors | Drug A model | Drug B model | Extraction of MAP priors | MCMC samples | Mixture approximation | Combination model with MAP priors for the new study | Robustification | Equivalence of MAP and MAC (advanced) | Appendix: Model specification | Combination BLRM (new study model) | Prior specification | Meta-analytic models for the historical data | Hierarchical model for combined data (MAC) | Session Info

Introduction | Abstract | Input file formats | Overview of steps | Standard genomic regions format | Install peakCombiner | An overview of a complete run | Prepare input data | Quick start | Load from sample sheet | Load from pre-loaded tibble | Load from GenomicRanges object | Explained in detail | Load from BED file | Working in 1-based space | Center and expand regions | Run center and expand | Explained in details | Define the 'center' | Expand from 'center' | Correct if expanding over chromsome boarders | Run function mutliple times | Filter regions | Filter genomic regions | Apply the right filters | Include chromsomes | Remove blacklisted sites | Filter for enrichment value | Select a defined number of regions | Combine regions | Run to combine regions | Define parameter to best combine regions | In how many samples should a region be found? | Which center to select for the consensus regions? | Session info | References

Overview | Required Packages | Traceability: annotating and saving plots and tables | Annotating figures | Graphics helpers | xgx theme | Confidence intervals | Nonlinear smoothing (e.g. Emax), and ordinal response smoothing | Nice log scale | Reverse log transform | Nice scale for percent change data | Scaling x-axis as a time scale