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
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
Analysis code used for Rabadam G, Neely J, et al. JCI Insight, 2024.
Repository for code and documentation for the Malian Data Science and Bioinformatics Network (MD-BioNet).
Docker containers used by cancer-seq-pipeline.
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
Oncology-focused variant prioritization pipeline for VEP-annotated VCF files derived from clinical NGS data.
Privacy-preserving hybrid RAG pipeline for clinical genomic variant interpretation — local LLM, LangGraph, pgvector, ClinVar, gnomAD, ClinGen, NCCN
This directory contains scripts for "Cell-free DNA Whole Genome Sequencing for Non-Invasive MRD Detection in Multiple Myeloma" by Abelman et al., 2025
A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
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
Korean population-aware genomic variant interpretation pipeline — deterministic ACMG/AMP classification with curate-then-narrate AI Clinical Board. Offline, research-use-only.
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