quality filtering tool for long reads

🔬 BEDOPS: high-performance genomic feature operations

This repository delivers end-to-end, code-first tutorials covering every layer of production-grade GenAI agents, guiding you from spark to scale with proven patterns and reusable blueprints for re…

BioMCP: Biomedical Model Context Protocol

BioMCP: Biomedical Model Context Protocol

Image Processing with Python

Material for the [BC]2 2019 workshop "Introduction to Machine Learning: opportunities for advancing omics data analysis"

some useful steps in tests 👣

a short-read polishing tool for long-read assemblies

Visualise networks and trees in Python, with style.

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting…

iLearn, a Python Toolkit and Web Server Integrating the Functionality of Feature Calculation, Extraction, Clustering, Feature Selection, Feature Normalization, Dimension Reduction and Model Constru…

Pan-genome wide association studies

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

A simple script to extract bioactivity data from the ChEBML database

A gap-closing software tool that uses long reads to enhance genome assembly.

Free, open source mental health communication web app to share experiences with loved ones

Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.

Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules

Community-Maintained Version of mordred

a molecular descriptor calculator

A web app to search pubmed

Build Real-Time Knowledge Graphs for AI Agents

Real Time Speech Transcription with FastRTC ⚡️and Local Whisper 🤗

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaboration with the RCSB Protein Data Bank.

Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.