Characterization of Germline variants

An Open Source Web Application for Genetic Data (SNPs) Data Crawling

Variant Agents: Multi-Agent Genomic Analysis

ClinVar Submission API Made Easy

PyGeneBe: A Python client seamlessly integrating with the GeneBe platform, offering efficient annotation of genetic variants through its API, while supporting pandas, VCF file formats, and HGVS parsing

automatic update Clinvar db for ANNOVAR

UPWARD: Uniting People Working Against Rare Diseases

An AI-driven genomic intelligence system delivering structured ClinVar interpretation and high-precision exon, intron, and gene queries using the Model Context Protocol (MCP).

Short Linear Motif (SLiM) Analysis in the context of human diseases

A bioinformatics pipeline to identify the best available PDB structures for all available variants for specified genes of interest

R script to 1) Extract missense variants that had been observed in "clinical testing" (as opposed to "literature only") in ClinVar. 2) Calculating movability and reappearance parameters using the aggregated and capped Invitae variant counts. 3) Apply the movability and reappearance parameters to ClinVar genes, calculating their movability- and reappearance-weighted impact score (MARWIS), as well as their difficulty-adjusted impact score (DAIS). 4) Rank ClinVar genes.

Identification of cancer-causing variants

Machine Learning-based Prediction of Pathogenicity for Protein Variants in ClinVar Database

Data repository for NeurIPS 2022 LMRL workshop paper.

Easy to use web interface for biologists to look for genetic variants and understand their deleteriousness using DITTO scores.

Cross-reference 23andMe raw variant file with ClinVar

ChemoProteomic-Detected Amino Acids (CpDAAs) to missense deleteriousness predictions and ClinVar pathogenic mutations

"NIHDataFetcher" is a GitHub repository with scripts for accessing and fetching data from various NIH databases like GEO and PubMed. It provides code examples to retrieve GEO datasets, search PubMed, and load ClinVar data. Ideal for researchers and data scientists working with biomedical information.

To predict cryptic cleavage sites in proteins with non-canonical signal peptides

Extending WES variant calling with ML to intelligently prioritise VUS for rare disease diagnostics. ROC-AUC: 0.79 | 439K high-risk variants flagged.

ClinVar-first VCF triage and reporting tool with optional PharmGKB enrichment.

Annoate a .vcf file with publicly-available data

The Amissense Tool analyzes and visualizes AlphaMissense pathogenicity scores, integrating AlphaFold structures and ClinVar data. It offers automated pipelines, visualizations, and versatile command-line utilities.

OpenDL is a non-profit Deep Learning research organisation discovering and accelerating artificial general intelligence studies to achieve competitive edge in the field of Legal, Health and Agriculture

neural networks to score PubMed search results for similarity to evidence abstracts from ClinVar or CIViC

GenAnalyzer is a web application designed for the analysis of protein sequences, mutation detection, and exploring their links to genetic diseases. Built using Flask, this tool integrates data from UniProt and ClinVar for efficient bioinformatics analysis.

🧬 Automated database management system for REEV genomic variant platform. Daily auto-updates for ClinVar & Mehari, compilation scripts for CADD & gnomAD. Docker-based deployment.

Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.

ML + LLM pipeline for genetic variant pathogenicity prediction (AUC 0.9949, 1.69M ClinVar variants) with SHAP explainability and clinical report generation via Llama 3 / Claude

Python Clinical Variant Tools This repository hosts Python scripts designed to streamline the retrieval of clinical variant information from authoritative sources such as ClinVar and DisGeNET. These tools facilitate efficient data extraction and analysis for researchers and professionals in the field of genetics and genomics.