Local models support for Microsoft's graphrag using ollama (llama3, mistral, gemma2 phi3)- LLM & Embedding extraction

This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.

Official repository for the Boltz biomolecular interaction models

Data validation using Python type hints

From annotated genomes to metabolic screening in large scale microbiotas

A grammar of graphics for comparative genomics

Detecting contamination in NGS data and multi-species analysis

Blazing-Fast Bioinformatic Operations on Python DataFrames

OVO, an open-source ecosystem for de novo protein design

A list of bioinformatic tools for working with Ribo-Seq data

Demystify RAG by building it from scratch. Local LLMs, no black boxes - real understanding of embeddings, vector search, retrieval, and context-augmented generation.

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Plasmid and primer design software

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Scripts and instructions to apply RiboTIE on Ribo-seq data

🦉 Data Versioning and ML Experiments

🪐 Markdown with superpowers: from ideas to papers, presentations, websites, books, and knowledge bases.

mbake is a Makefile formatter and linter. It only took 50 years!

A pipeline to generate and benchmark synthetic datasets as described in Sergi et al., 2024.

Package management made easy

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

Accurate and rapid RiboRNA sequences Detector based on deep learning

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction