Inferring variant-specific reproduction numbers from case counts and sequencing data
☆45Jul 6, 2026Updated 2 months ago
Alternatives and similar repositories for rt-from-frequency-dynamics
Users that are interested in rt-from-frequency-dynamics 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 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
- Code for "Ranking the effectiveness of worldwide COVID-19 government interventions"☆22Nov 17, 2022Updated 3 years ago
- A tool for exploring large trees in the browser☆133Updated this week
- Flu Scenario Modeling Hub☆12Aug 20, 2026Updated 2 weeks ago
- Migrating from SAS to R☆16Feb 23, 2024Updated 2 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.
- Heat-related mortality in Europe during the summer of 2022☆10Sep 10, 2023Updated 2 years ago
- Calculates the age-stratified infection fatality ratio (IFR) of COVID-19☆107Jun 21, 2021Updated 5 years ago
- In this work, we use S-gene target failure (SGTF) as a proxy of variant status combined with reported case counts to explore the evidence…☆15Aug 20, 2026Updated 2 weeks ago
- Code to test Rt estimates against synthetic data☆18Nov 30, 2020Updated 5 years ago
- Points of Significance: Adding realism to the SIR model for infectious disease epidemics☆13Nov 30, 2021Updated 4 years ago
- Pyro models of SARS-CoV-2 variants☆80Jul 26, 2024Updated 2 years ago
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆23Sep 29, 2025Updated 11 months ago
- Initialization is critical for preserving global data structure in both t-SNE and UMAP☆24Feb 3, 2021Updated 5 years ago
- Sequence lineage information extracted from RKI sequence data repo☆23May 17, 2022Updated 4 years ago
- 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.
- The ARTIC fieldbioinformatics pipeline☆136Aug 26, 2026Updated last week
- A scraper for bioRxiv☆12Apr 12, 2023Updated 3 years ago
- Scalable relaxed clock phylogenetic dating☆29Jul 5, 2026Updated 2 months ago
- Nextstrain build for avian influenza viruses☆29Aug 3, 2026Updated last month
- International SARS-CoV-2 surveillance☆39May 19, 2023Updated 3 years ago
- RSV-A lineage definitions and proposals☆16Nov 9, 2025Updated 9 months ago
- ☆51Mar 11, 2022Updated 4 years ago
- Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data☆34Oct 25, 2013Updated 12 years ago
- Programmatically interact with the GISAID database.☆83Aug 5, 2025Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- A phylogeny dating method using least-squares algorithms and criteria☆34Oct 25, 2024Updated last year
- R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.☆21Mar 5, 2023Updated 3 years ago
- Extract raw underlying data from PDF figures☆55Jan 13, 2026Updated 7 months ago
- LaTeX template of graduate Thesis [University of Chinese Academy of Sciences]☆12Nov 7, 2017Updated 8 years ago
- Coalescent simulation and likelihood for phylodynamic inference☆17May 15, 2025Updated last year
- Welcome to the StrainHub Repo - Files and Data - StrainHub Online:☆18Jun 26, 2022Updated 4 years ago
- OpenBabel wrapper package for R☆10Mar 12, 2026Updated 5 months ago
- Scrapping tool for GISAID data regarding SARS-CoV-2☆42May 22, 2023Updated 3 years ago
- 🦠 List of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencin…☆46May 21, 2020Updated 6 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Utility to alias and dealias pango lineages☆23Dec 18, 2023Updated 2 years ago
- Covid-19 epidemiology - data and analysis☆11Dec 7, 2023Updated 2 years ago
- General purpose population genetics software☆18Jul 15, 2019Updated 7 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆45Jul 2, 2026Updated 2 months ago
- The Zika bioinformatics pipeline☆37Mar 29, 2020Updated 6 years ago
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2026, Bioinformatics)☆43Updated this week
- An example of how to create an R package that utilizes C++ code that calls Fortran code☆13Jan 31, 2023Updated 3 years ago