Characterization of Germline variants

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

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

Identification of cancer-causing variants

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

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

"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.

Annoate a .vcf file with publicly-available data

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

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.

Flask-based webapp and API used to query and generate tabular reports of data relating to clinically-observed genetic variants

Automate ClinVar lookup of sequencing results from TermoFischer Ion Torrent machines.

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.