Contents

1 Overview

This is an indexed and lightly annotated catalog of packages developed in our group. Many of these packages need additional support (unit tests, vignette improvements, migration of large serializations to ExperimentHub or AnnotationHub). Notes on development priorities are in the next section, followed by the list of packages.

2 Development priorities as of June 23 2019

2.1 Overall

Unit testing coverage needs to be addressed for all packages.

2.2 Cancer genomics

  • The vignette of BiocOncoTk includes a number of outreach tasks that have not been addressed well. Cleaner interfaces to cBioPortal, TIES, additional work on CPTAC…
  • The nested dependency structure of blocks in ivygapSE data needs to be addressed to support valid inference on donor-level covariate associations
  • The tumex5 package demonstrates MAE with HSDS back end and more work is needed to broaden scope of assay coverage and back end flexibility

3 Package references

3.2 Scalable data access (co-authored)

3.3 Human genetics

3.4 Human genomics

3.5 Ontology and text mining

3.6 Machine learning

3.7 Curated data

3.8 Epidemiology and biostatistics