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

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

R-based NGS tertiary analysis pipeline: BAM → ESMO 2024 clinical report with OncoKB, PubMed/Scopus literature, ESCAT classification

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

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 state-space CNV Caller with Disease Profiling

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.

Workflows relating to the GA clinical genomics project

Docker containers used by cancer-seq-pipeline.

Repository for code and documentation for the Malian Data Science and Bioinformatics Network (MD-BioNet).

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

LLM-assisted genomic variant interpreter integrating ClinVar, Ensembl VEP, and COSMIC

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.

A simple xml-to-csv parser for Foundation Medicine XML reports

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

PRISM: Pharmacogenomic Resolution via Integrated Star-allele Matching — Production-grade multi-caller PGx star allele calling pipeline with evidence-weighted consensus, CPIC drug recommendations, HL7 FHIR R4, and GA4GH VRS 1.3 output

MCP server grounding gene/disease/variant questions in ClinGen curated evidence (gene-disease validity, gene dosage, clinical actionability, variant pathogenicity/ERepo)