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

Functions for working with the Human Phenotype Ontology data

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

A state-space CNV Caller with Disease Profiling

A modular registry for trustworthy, evidence-based genomic analysis powered by Model Context Protocols (MCPs). Bridging AI and clinical genomics with traceable, validated data retrieval.

Workflows relating to the GA clinical genomics project

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

Docker containers used by cancer-seq-pipeline.

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

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

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

Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

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

A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using GATK4, SnpSift, VEP and genmod. Designed to be used after human_genomics_pipeline.

AI/ML bioinformatics portfolio covering mutation impact, biomarkers, SNP mapping, regulatory genomics, expression modeling, and TF binding

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 Shiny interface to filter and identify variants of interest from whole exome data

🧬 Explore GeneFoundry, a modular registry delivering trustworthy genomic analysis through validated data, tackling AI's "hallucination" challenge.