Philipp Angerer

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

The paper introduces anndata, a Python package for handling annotated data matrices, providing features like sparse data support and a PyTorch interface.

This paper introduces methods to identify globally and locally relevant genes in nonlinear low-dimensional embeddings of single-cell RNA-seq data, demonstrating their versatility across datasets and embedding techniques.

FASTGenomics provides a secure, flexible, and user-friendly analytical ecosystem for single-cell transcriptomics data.

Python toolkit Scanpy, built on HDF5-backed AnnData, achieves speedups of 5 to 16 times over Cell Ranger's R kit and clusters 1.3 million cells without subsampling.

The paper introduces destiny, an R package for diffusion maps in single-cell data, with efficient nearest-neighbour approximation and noise modeling for large datasets.