automatic update Clinvar db for ANNOVAR

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

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

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.

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.

Identification of cancer-causing variants

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

Web application to analyse ClinVar marker frequencies in populations over time. R-shiny application for population genetics analysis.

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

"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.

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

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

Data repository for NeurIPS 2022 LMRL workshop paper.

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

Characterization of Germline variants

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

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

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 r…

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