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.

cross-species analysis of cell identities, markers and regulations

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

A python package for qPCR primers design, check, annotate and visualize.

PLM based active learning model for protein engineering

《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被70多个国家的500多所大学用于教学。

GeneCompass

User-friendly WebUI for LLMs (Formerly Ollama WebUI)

Get up and running with Llama 3, Mistral, Gemma 2, and other large language models.

Enchanted is iOS and macOS app for chatting with private self hosted language models such as Llama2, Mistral or Vicuna using Ollama.

Open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place.

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

This is a Gymrek lab version HipSTR.

R package to draw syntenic plots in 3 different styles

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

Tools for merging 1000 Genomes calls

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets

predicting peptide-protein interactions

PopSTR - A Population based microsatellite genotyper

Molecular generative framework for protein-protein interface inhibitors

Identify and find telomeres, or telomeric repeats in a genome.

A genome completeness evaluation tool based on miniprot

Code for Command-Line Rust (O'Reilly, 2022, ISBN 9781098109417) https://learning.oreilly.com/library/view/command-line-rust/9781098109424/

Identifying peptide-receptor interactions using AlphaFold-Multimer

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities