blab / rt-from-frequency-dynamics
Inferring variant-specific effective reproduction numbers from combined case and sequencing data
☆46Updated this week
Related projects ⓘ
Alternatives and complementary repositories for rt-from-frequency-dynamics
- Resources for Influenza Research☆23Updated 2 years ago
- ☆26Updated 3 years ago
- ☆25Updated last year
- Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline f…☆25Updated last year
- R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.☆20Updated last year
- Helix® COVID-19 Surveillance☆16Updated 2 years ago
- Inference framework for serological data☆16Updated this week
- Calculates the age-stratified infection fatality ratio (IFR) of COVID-19☆108Updated 3 years ago
- Extract raw underlying data from PDF figures☆56Updated 9 months ago
- A web platform to detect and analyze variants of SARS-CoV-2☆61Updated this week
- Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater☆20Updated this week
- Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States☆27Updated 2 months ago
- A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.☆19Updated last month
- ☆17Updated last month
- Code to test Rt estimates against synthetic data☆16Updated 3 years ago
- Analysis of global migration patterns of seasonal influenza viruses☆22Updated 5 years ago
- Heatmap-integrated Decision Tree Visualizations☆57Updated last year
- An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources☆59Updated 2 years ago
- A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV…☆36Updated last week
- Pathogen evolution, selection and immunity☆47Updated 8 months ago
- Projects on COVID-19 topic of genomic sequencing - mostly DataViz☆50Updated last week
- National and subnational estimates of the time-varying reproduction number for Covid-19☆34Updated 2 years ago
- ☆12Updated 2 years ago
- Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model wit…☆58Updated last week
- outbreaks: an R package compiling disease outbreak data☆51Updated last year
- Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. …☆100Updated 3 years ago
- Disease outbreak reconstruction from epidemiological and genetic data☆31Updated last month
- The Public Health Environmental Surveillance Open Data Model (PHES-ODM, or ODM). A data model, dictionary and support tools for environme…☆54Updated 3 weeks ago
- An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wh…☆37Updated last year
- Code for reconstructing influenza dynamics from surveillance data using evidence synthesis techniques☆19Updated 2 years ago