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Work in Progress:�Bioconductor and the HCA

Martin.Morgan@RoswellPark.org

20 February 2019

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Scope

Funding

  • One year seed funding
  • 8 Projects
  • Fully ‘open’ development, initiated by Aaron Lun

Aims

  1. HCA Access
  2. Data representations
  3. Scalable preprocessing pipelines
  4. Scalable statistical routines
  5. Ontology

Symposium

  • Near end of seed funding, so projects are approaching maturity
  • Great opportunity to
    • Summarize progress
    • Identify challenges & opportunities
    • Share with a broader community!

‘Work in progress’

  • Rough and challenging edges, particularly in scalability

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People and collaborations

Data access and annotation

Scalable interactivity in R

Scalable statistical procedures

John Marioni, Aaron Lun

Martin Morgan, Daniel van Twisk, Marcel Ramos

Wolfgang Huber, Mike Smith

Raphael Gottardo, Mike Jiang,Greg Finak

Vince Carey, Aedin Culhane

Kasper Hansen, Peter Hickey

Davide Risso, Stephanie Hicks, Elizabeth Purdom

Rafael Irizarry, Christina Kendziorski, Keegan Korthauer, Meromit Singer

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Acknowledgements�(Martin)

A portion of this work is supported by the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.

Research reported in this presentation was supported by the NHGRI and NCI of the National Institutes of Health under award numbers U41HG004059, U24CA180996, and U24CA232979. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

This work was performed on behalf of the SOUND Consortium and funded under the EU H2020 Personalizing Health and Care Program, Action contract number 633974.