Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline fits
☆25Apr 24, 2023Updated 3 years ago
Alternatives and similar repositories for LineageExplorer
Users that are interested in LineageExplorer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- International SARS-CoV-2 surveillance☆39May 19, 2023Updated 3 years ago
- ☆10May 28, 2023Updated 3 years ago
- ☆20Apr 9, 2021Updated 5 years ago
- Bayesian Modelling in Epidemiology Case Line Lists☆14Oct 7, 2025Updated 10 months ago
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆17Aug 20, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Descriptive summaries of covid data for Belgium☆10Apr 23, 2021Updated 5 years ago
- Short course on parametric survival analysis☆15Aug 5, 2026Updated 3 weeks ago
- Estimate epidemiological delay distributions with brms☆16Updated this week
- Covid-19 epidemiology - data and analysis☆11Dec 7, 2023Updated 2 years ago
- Official place for proposals and details around monkeypox virus lineage designations☆23Jul 7, 2026Updated last month
- Additional censored event tools for Distributions.jl☆15Updated this week
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 8 months ago
- ☆29May 19, 2026Updated 3 months ago
- Programmatically interact with the GISAID database.☆83Aug 5, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- An R package for the analysis of infectious disease transmission data☆10Nov 8, 2021Updated 4 years ago
- ☆21Apr 2, 2025Updated last year
- ☆44Apr 13, 2026Updated 4 months ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 4 years ago
- Ecological forecasting using Dynamic Generalized Additive Models with R 📦's {mvgam} and {brms}☆41Mar 28, 2025Updated last year
- ☆27Feb 25, 2021Updated 5 years ago
- A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.☆21Sep 1, 2025Updated 11 months ago
- Reproducible workflow for SARS-CoV-2 recombinant sequence detection.☆18May 15, 2023Updated 3 years ago
- ☆12Sep 11, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Data and code to support Barnard et al., Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era, Nat…☆12Aug 31, 2022Updated 4 years ago
- R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parame…☆38Jul 1, 2026Updated 2 months ago
- ☆22Jul 25, 2026Updated last month
- Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on red…☆13Dec 18, 2022Updated 3 years ago
- Material for the lecture Statistical Computing☆12Jan 1, 2026Updated 7 months ago
- Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States☆27Aug 14, 2025Updated last year
- An R package and Bayesian generative model to estimate epidemiological parameters from wastewater concentration measurements over time.☆27Updated this week
- Informal summaries of notable SARS-CoV-2 lineages☆111Jun 1, 2026Updated 2 months ago
- Derive social mixing matrices from survey data.☆44Updated this week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (RE…☆19May 9, 2024Updated 2 years ago
- ☆14Oct 20, 2023Updated 2 years ago
- Sequence lineage information extracted from RKI sequence data repo☆23May 17, 2022Updated 4 years ago
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆14May 23, 2023Updated 3 years ago
- Full code and models for paper describing a hierarchical Bayesian GAM for the BBS☆13Oct 26, 2020Updated 5 years ago
- Fit stochastic differential equation models with time-varying parameters☆15Jul 30, 2026Updated last month
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago