Yuji Okano

BasalCell provides a project scaffold generator to integrate R and Python ecosystems, enabling reproducible, multi-language bioinformatics workflows with version control and CI/CD.

The paper identifies how heterogeneous single-cell observations distort manifold-based inference and proposes topological stability descriptors to assess reliability.

The paper evaluates experimental design in Perturb-seq, finding that correlated designs are robust in systems with signal amplification and introduces a metric to predict optimal designs.

The paper improves a graph-based method for evaluating cell cluster identities by addressing practical implementation issues and enhancing utility with new features and techniques.