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Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)

AI coding assistant for JupyterLab with agent mode, supporting arbitrary LLM providers (2025+)

High-accuracy PDF→Markdown/JSON/HTML conversion, specialized for tables/formulas/code blocks with benchmark scripts

Automated pipeline for proteome-scale protein-protein interaction screening with AlphaFold-Multimer and AlphaFold 3, supporting flexible inputs (UniProt IDs, FASTA, residue regions, multimers, AF3 JSON features) and integrated downstream analysis for hit prioritization (Kosinski Lab, EMBL, Nature Protocols 2024, 317+ stars, GPL-3.0)

Neural network-based cryo-EM heterogeneous reconstruction, modeling continuous 3D structure distributions from single-particle images, with CryoDRGN-ET extending to in-cell cryo-electron tomography (MIT CSAIL, Nature Methods 2021/2024)

Self-hostable scientific claim-verification and literature-review tool combining Semantic Scholar retrieval, bibliometric scoring, and LLM-based evidence synthesis for large-batch validation workflows

Fast spike sorting with drift correction for extracellular electrophysiology, enabling universal neural spike sorting via deep learning on high-density neural probe recordings (MouseLand, 609+ stars)

Convert PDF files into editable slides with three lines of code

Single-cell BERT for gene expression