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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)

A Simulation Tool for Fractured and Deformable Porous Media.

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

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.

Behavioral and neuroimaging experiments.

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)

an automated workflow for the generation and storage of DFT calculations for organic molecules.

PathBench-MIL is a comprehensive, flexible benchmarking/AutoML framework for multiple instance learning in histopathology

General purpose tools for high-throughput catalysis.

Convert PDF files into editable slides with three lines of code

Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences.

file format conversion in Biopython in a convenient way.

AlphaPickle is a Python tool that converts AlphaFold and ColabFold output files into user-friendly CSV files and plots, enabling easy analysis and visualization of protein prediction data without requiring programming expertise. It processes .pkl, .json, and PDB files to extract and visualize metrics like pLDDT and PAE.

Single-cell BERT for gene expression

NuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.

Filtering and trimming of long read sequencing data.

qam is a Python library and command-line tool to compute 3D surface-distances for evaluating liver ablation/tumor completeness based on segmentation images.