-
CoVEO PCR primers mutations
Mentes et al, Scientific Reports: 2022
Python-based pipeline for identifying SARS-CoV-2 mutations overlapping PCR primer binding sites and assessing their potential diagnostic impact.
github.com/csabaiBio/coveo_pcr_primers2021 -
SARS-CoV-2 RBD deep mutational AlphaFold2 structures carry phenotypic information
Kilim et al, 2023, Scientific Data
Scripts and helper notebooks used to generate, process and organise AlphaFold2 structure predictions and associated phenotypic annotations for single-point mutants in the SARS-CoV-2 receptor-binding domain (RBD).
github.com/csabaiBio/RBD-AlphaFold2-structures-and-phenotypic-information -
CoVEO variant explorer
[Rahman et al, 2024, Microbial Genomics] (https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001188#R38)
Shiny application for visualizing SARS-CoV-2 variant prevalence, mutation patterns, and diagnostic primer mismatches using CoVEO<>br> github.com/csabaiBio/coveo_pcr_primers2021 -
KooplexQuery: Database exploration with AI agents: Sewage Database and Viralprimer Database
github.com/kooplex/kooplexQuery -
CoVEO VCF database
Rahman et al, 2024, Microbial Genomics
R scripts and SQL schema for importing, processing and querying SARS-CoV-2 variant call (VCF) files in a relational database environment.
github.com/pkrisz5/vcf_database -
Kooplex Platform
Visontai et al., arxiv.org/pdf/1911.09553, Kooplex: collaborative data analytics portal for advancing sciences,
Collaborative platform for storing and analysing data, and publishing interactive reports and applications
github.com/kooplex -
Sewage database
A comprehensive database for biological data derived from sewage in five European cities
A multi-layered dataset from sewage across five European cities in an SQL database.
https://github.com/nyeszka/sewage_db -
SewageGPT
A Case Study Using Sewage Metagenomic Data for Assessment of Text-to-SQL Capabilities in Large Language Models, Papp et al.
SewageGPT is a customized ChatGPT that is connected with a PostgreSQL database containing information about metagenomic analysis of sewage samples.
github.com/pkrisz5/SewageGPT -
ViralPrimer