Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.
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Updated
Nov 21, 2018
Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.
neural networks to score PubMed search results for similarity to evidence abstracts from ClinVar or CIViC
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.
An R package for interpreting genetic variants according to the ACMG guidelines.
Web application to analyse ClinVar marker frequencies in populations over time. R-shiny application for population genetics analysis.
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.
Annoate a .vcf file with publicly-available data
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
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
Data repository for NeurIPS 2022 LMRL workshop paper.
Identification of cancer-causing variants
To predict cryptic cleavage sites in proteins with non-canonical signal peptides
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.
Easy to use web interface for biologists to look for genetic variants and understand their deleteriousness using DITTO scores.
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…
Short Linear Motif (SLiM) Analysis in the context of human diseases
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