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.
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
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
Oncology-focused variant prioritization pipeline for VEP-annotated VCF files derived from clinical NGS data.
AI/ML bioinformatics portfolio covering mutation impact, biomarkers, SNP mapping, regulatory genomics, expression modeling, and TF binding
Unified R platform for molecular pathology data — parse NGS files (VCF, BAM, FASTQ), XML/PDF reports, and clinical data into a queryable database with an interactive Shiny app for clinical exploration and visualization.
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