Software

The page lists open source software. Beyond what is listed, I have created and contributed to software for computational physics, causal inference, and to proprietary software for industry (machine learning, data science, data management, photovoltaics simulations).

Initial conception & development

  • Scanpy: Single-cell analysis in Python
  • anndata: Annotated data
  • PAGA: Mapping out the global connectivity structure of manifolds

Supervision of lead developer

  • scvelo: Dynamic model for RNA velocity for single cells
  • scgen: Generative modeling of single-cell perturbation response

Major contributions

  • Data Science Bowl 2017: major contributions to 7th prize (out of 2400 participating teams) winning deep learning pipeline in highest endowed ($1M prize money) machine learning competition 2017