A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

A customizable pipeline for multimodal data extraction from MIMIC-IV!

A single interface to use and evaluate different agent frameworks

Official GIT version of ZENBU genomics visualization system. https://sourceforge.net/projects/zenbu/

Benchmark gene representations from different model families

🤖 A Python library for learning and evaluating knowledge graph embeddings

Tool for creating and editing annotation tables in ARCs.

Bioconductor package to access the harmonized metadata through ontology

implicit pangenome graph

WFA-lib: Wavefront alignment algorithm library v2

Clojure library and command line application for converting CSV to RDF. An implementation of the W3C CSVW specifications

Python tools for identification and distribution of reference sequences and sequence collections

SPARQList: Repository server for working SPARQL snippets

tRNA Analysis of eXpression

A tool for detecting and quantifying alternative splicing with RNA-seq

Variant Calling for the HPRC Release 2

Convert bioinformatics file formats to Zarr

Build AI-native spreadsheets. Univer is a full-stack framework for creating and editing spreadsheets on both web and server. With Univer Platform, Univer Spreadsheets is driven directly through nat…

Data Integration Visual Exploration (DIVE)

Convert vcf in parquet

Generic SDK and CLI for GA4GH API services

Resources for the KG course at IDS, Maastricht University

Visualising / Exploring Linked Data (SPARQL Construct queries) in Virtual Reality.

OctoTools: An agentic framework with extensible tools for complex reasoning

Quantum circuit optimization with deep learning

Ontology lifecycle management

Work with bioinformatic files using Arrow, Polars, and/or DuckDB