Deliverables

  1. Technical report describing the data structure and methods for operating on screening data. PDF
  2. Open-source software for the standardized application of existing methods in liquid biopsy data analysis, supported by online catalogue of existing methods and data resources. PDF
  3. Open-source software CAUSEXPR, to prioritize likely causal mutations from genotype and gene expression. PDF
  4. Open-source software CAUSAMET and BIOMARK. PDF
  5. Technical report on approaches to outlier detection in patient ‘omics data. PDF
  6. Open-source software that implements causal stability ranking for high-dimensional genotype data. PDF
  7. Technical report on disease classification based on multilevel data integration. PDF
  8. Technical report and software for predictive modelling of drug response and detection of outlier samples. PDF
  9. Open-source software supporting the molecular tumour characterization pipeline and predicting perturbed pathways. PDF
  10. Technical report on new disease entities that were identified using novel statistical methods. PDF
  11. Open-source software implementing an updated version of Renjin that supports the major Bioconductor packages; a code library of benchmarks; and a technical report describing the most significant performance bottlenecks. PDF
  12. Technical report with evaluation of performance improvement or regression from D9.2. PDF
  13. Technical report with definitions and best practice guidelines; and software package for simulation of experimental design and choice of validation sites in cancer genomics. PDF
  14. Database of solved cases. PDF
  15. Open-source software implementing end-to-end analysis and integrating the results from T1.1-1.5. PDF
  16. Technical report on existing and novel methods. PDF
  17. Open-source software to estimate structured sparse models from multi-omics data. PDF
  18. Open-source software that implements tumour diversity time series analysis. PDF
  19. Technical report describing the design of re-capture platform for deep sequencing and validation. PDF
  20. Technical report on biomarkers analysed with transcriptome and metabolome data and technical report on novel pathomechanisms. PDF
  21. White paper describing software design principles and implementations; and open-source software implementation of SOUNDHub (annotation) and SOUNDData (experiment data) services and clients, with specific development of controlled and federated data access. PDF
  22. SOUNDData and SOUNDHub public data resources. PDF
  23. Open-source software implementing InteractiveReports for displaying and scripting reproducible workflows; and a software catalogue of standard templates for informed decision-making. PDF
  24. Website of Interactive Reports for select outcomes of WP2. PDF
  25. Software package for automated benchmarking. PDF