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
Alternatives and similar repositories for R-outbreak-info
Users that are interested in R-outbreak-info are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SARS-CoV-2 genome data analysis☆10Dec 6, 2025Updated 4 months ago
- Import script needed to build FluPRINT database from source☆11May 23, 2019Updated 6 years ago
- ☆22Mar 5, 2025Updated last year
- A package containing several useful R-functions for reading and plotting the results of Birth-Death Skyline (BDSKY) runs in BEAST2.☆12Nov 28, 2018Updated 7 years ago
- Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater☆21Apr 10, 2026Updated last week
- 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.
- Assists in making queries to CDC Wonder API☆29Mar 15, 2024Updated 2 years ago
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2026, Bioinformatics)☆42Mar 24, 2026Updated 3 weeks ago
- Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification☆15Sep 27, 2023Updated 2 years ago
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics☆20Jan 13, 2019Updated 7 years ago
- ☆18Jan 29, 2022Updated 4 years ago
- ☆19Nov 24, 2025Updated 4 months ago
- This repo contains the code for a shiny app that allows for visualization of subset phylogenetic trees☆15Jan 9, 2019Updated 7 years ago
- Scenario-based health impact projections of the war in Gaza (2023-2024)☆24Jan 26, 2026Updated 2 months ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆24Apr 11, 2026Updated last week
- causact: R package to accelerate computational Bayesian inference workflows in R through interactive visualization of models and their o…☆48Sep 12, 2025Updated 7 months ago
- GCtree: phylogenetic inference of genotype-collapsed trees☆18Aug 27, 2024Updated last year
- BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.☆21Aug 11, 2025Updated 8 months ago
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Apr 5, 2022Updated 4 years ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆18Nov 24, 2025Updated 4 months ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆18Apr 28, 2023Updated 2 years ago
- Model-based time series clustering using variational inference.☆12Oct 28, 2018Updated 7 years ago
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆17Nov 10, 2023Updated 2 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.
- Pyro models of SARS-CoV-2 variants☆77Jul 26, 2024Updated last year
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 7 months ago
- R tools for posterior analyses using BEAST☆20Apr 10, 2019Updated 7 years ago
- scripts for analysis associated with Cas9Enrichment publication☆12Feb 10, 2020Updated 6 years ago
- Analysis of global migration patterns of seasonal influenza viruses☆22Jul 24, 2019Updated 6 years ago
- A R statistical software package for estimating attributable influenza morbidity & mortality☆13Jun 6, 2019Updated 6 years ago
- B-cell repertoire and clonal family tree explorer☆17Apr 3, 2026Updated 2 weeks ago
- Repository for Global.health: a data science initiative to enable rapid sharing of trusted and open public health data to advance the res…☆41Apr 17, 2023Updated 3 years ago
- An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads☆13Apr 8, 2026Updated last week
- 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.
- Umbrella documentation project for Nextstrain☆18Updated this week
- DeepNovo workflow of neoantigen discovery by personalized de novo sequencing.☆12Nov 26, 2020Updated 5 years ago
- A repo with supplementary material for a manuscript on the origin of SARS-CoV-2 origins☆11Jun 26, 2020Updated 5 years ago
- Reproducible workflow for SARS-CoV-2 recombinant sequence detection.☆18May 15, 2023Updated 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…☆37Updated this week
- A Python library for generating random phylogenetic trees and related data☆13Jul 4, 2022Updated 3 years ago
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.☆17Updated this week