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Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"

R 14 1 Updated Feb 10, 2025

openpilot is an operating system for robotics. Currently, it upgrades the driver assistance system on 275+ supported cars.

Python 52,491 9,454 Updated Feb 17, 2025

A reactive notebook for Python — run reproducible experiments, execute as a script, deploy as an app, and version with git.

Python 10,548 390 Updated Feb 17, 2025

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

Python 86 11 Updated Jun 25, 2023

Protein function prediction in bacteria using genomic context

Python 2 Updated Feb 16, 2025

Synteny-aware gene function prediction for bacteria using protein embeddings

Python 4 2 Updated Jan 8, 2025

Scalene: a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals

Python 12,446 403 Updated Jan 27, 2025

A high-performance, zero-overhead, extensible Python compiler with built-in NumPy support

Python 15,414 528 Updated Feb 15, 2025

RPA primer and CRISPR-Cas12a guide RNA design for diagnostics

Shell 4 Updated Feb 10, 2025

Organism-specific interpretation of AMR genotypes

Python 10 2 Updated Mar 13, 2024

Metadata template for genomic surveillance of bacterial pathogens for vaccine and AMR purposes

4 1 Updated Apr 26, 2024

Drop in a screenshot and convert it to clean code (HTML/Tailwind/React/Vue)

Python 68,380 8,396 Updated Feb 4, 2025

A Generative Pre-Trained Transformer Package for Pangenomes

Python 50 4 Updated May 17, 2024

Biological foundation modeling from molecular to genome scale

Jupyter Notebook 1,281 160 Updated Dec 18, 2024

Auxiliary Common Lisp Utilities for Generative Art

Common Lisp 69 Updated Jul 19, 2024

A repo to evaluate various LLM's chess playing abilities.

Python 76 18 Updated Apr 12, 2024

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

C++ 85 17 Updated Nov 25, 2024

Distribute and run LLMs with a single file.

C++ 21,730 1,136 Updated Jan 30, 2025

Successful Job Applications and Grants

731 130 Updated Jan 2, 2025

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Python 27 12 Updated Feb 16, 2025

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

Python 34 14 Updated Feb 14, 2025

The most used Rust library for date and time handling.

Rust 1,150 283 Updated Feb 12, 2025

Python programs for processing GFF3 files

Python 96 27 Updated Mar 27, 2024

tree visualization for tree + annotation data

Python 28 3 Updated Feb 16, 2025
C++ 9 Updated Aug 23, 2023

Snakemake workflow management system and CLI generation tool

Python 52 4 Updated Jan 29, 2025

Generate captions for images with Salesforce BLIP

Python 120 10 Updated Jul 11, 2024

NCBI Pathogen Detection Portal toolkit

Perl 11 Updated Sep 6, 2023

Fully convolutional deep learning variant effect predictor architecture

Python 23 4 Updated Jan 3, 2024

Efficient evolution from protein language models

Python 187 45 Updated Aug 26, 2023
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