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:
- Data and files from the May 25, 2021 SARS-CoV-2 viral load and infectiousness paper☆10Jan 14, 2022Updated 4 years ago
- International SARS-CoV-2 surveillance☆38May 19, 2023Updated 3 years ago
- ☆10May 28, 2023Updated 3 years ago
- Joint Bayesian generative Turing model for the 2026 DRC BVD outbreak. Combines exports, deaths and reported suspected cases (with ascerta…☆15Updated this week
- ☆20Apr 9, 2021Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆17Sep 19, 2026Updated last month
- Descriptive summaries of covid data for Belgium☆10Apr 23, 2021Updated 5 years ago
- Bayesian Modelling in Epidemiology Case Line Lists☆14Oct 7, 2025Updated last year
- 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
- Short course on parametric survival analysis☆15Oct 15, 2026Updated 2 weeks ago
- Covid-19 epidemiology - data and analysis☆11Dec 7, 2023Updated 2 years ago
- Estimate epidemiological delay distributions with brms☆17Updated this week
- Additional censored event tools for Distributions.jl☆15Updated this week
- Official place for proposals and details around monkeypox virus lineage designations☆23Jul 7, 2026Updated 3 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Repository for EpiFusion, an infectious disease modelling framework built on the principles of phylodynamics and epidemiology☆16Apr 1, 2026Updated 6 months ago
- Data and code used to generate figures to describe SARS-CoV-2 VOI lineage B.1.620 in Europe/Lithuania.☆11Sep 8, 2021Updated 5 years ago
- app to collapse Pango lineages for reporting☆14Oct 2, 2026Updated 3 weeks ago
- An R package for the analysis of infectious disease transmission data☆10Nov 8, 2021Updated 4 years ago
- Reproducible workflow for SARS-CoV-2 recombinant sequence detection.☆18May 15, 2023Updated 3 years ago
- Programmatically interact with the GISAID database.☆83Aug 5, 2025Updated last year
- A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.☆21Oct 10, 2026Updated 3 weeks ago
- ☆29Oct 7, 2026Updated 3 weeks ago
- Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.☆10Jul 22, 2022Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ☆44Apr 13, 2026Updated 6 months 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
- Derive social mixing matrices from survey data.☆44Sep 28, 2026Updated last month
- 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
- 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
- Results from a model of global SARS-CoV-2 lineage competition☆40Dec 17, 2025Updated 10 months ago
- ☆26Jul 25, 2026Updated 3 months ago
- R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parame…☆39Sep 28, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- 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
- ☆13Sep 11, 2024Updated 2 years ago
- Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States☆27Aug 14, 2025Updated last year
- ☆14Oct 20, 2023Updated 3 years ago
- Sequence lineage information extracted from RKI sequence data repo☆23May 17, 2022Updated 4 years ago
- Multivariate (multi-response) ensemble learning☆10Jul 22, 2026Updated 3 months ago
- Informal summaries of notable SARS-CoV-2 lineages☆112Jun 1, 2026Updated 4 months ago