clinical-genomics

ClassifyCNV: a tool for clinical annotation of copy-number variants

API-first variant triage pipeline combining genomic filtering, annotation, and LLM-driven interpretation for clinical genomics workflows

Functions for working with the Human Phenotype Ontology data

Multi-source germline variant annotation pipeline

Genesis: Multi-Modal Agentic AI for Cancer Variant Effect Prioritization

R pipeline for cancer genomics: BAM/VCF to ESMO-compliant clinical reports with OncoKB, variant classification (ESCAT/AMP-ASCO-CAP), CNV, fusion, TMB, MSI, and PubMed/Scopus literature retrieval

Introduction to Human Next Generation Sequencing Projects and GWAS analysis offered to ACE Mali students. GWAS demo utilizing PLinK, a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses.

A proof-of-concept bioinformatics platform designed to translate complex genomic reports into clear, patient-friendly clinical interpretations, bridging computational genomics with accessible healthcare communication and supporting more understandable interpretation of genomic information.

Clinical AMR & Virulence Gene Profiling — Klebsiella pneumoniae (CARD/ResFinder Pipeline)

Comprehensive Sanger sequence analysis and clinical reporting tool. Identifies SNVs and Indels precisely while keeping your genetic data secure locally.

Workflows relating to the GA clinical genomics project

Explore genomes across the world 🧬🌍🧬

🧬 Convert FoundationOne genomic reports to cBioPortal OncoPrinter format — visualize mutations, CNVs, and fusions

A local API-based biological engine that uses Tracy for sequence alignment and VEP for variant annotation. Built with Python for computational biology and bioinformatics analysis.

Clinical genomic analysis with 105 curated agent skills. Research overview, results and invitation-based web access. System code is not publicly released.

A state-space CNV Caller with Disease Profiling

Analysis code used for Rabadam G, Neely J, et al. JCI Insight, 2024.

Materials for ACE course on Genetic Linkage Analysis.

Docker container to download dbNSFP 'database' and wrangle it into a format suitable for pipeline annotation process

Using Protein Language Models to compute Variant Effect Predictions across population-scale populations.