HopkinsIDD / phylosamp
The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.
☆12Updated last year
Related projects: ⓘ
- Estimating time trees from very large phylogenies☆24Updated last month
- ☆15Updated last week
- An automated pipeline for retrieving orthologous DNA sequences from GenBank in R☆23Updated 2 months ago
- phylogenetic networks using ggplot2 and ggtree☆11Updated 4 years ago
- Metagenomics calibration R package☆18Updated 2 years ago
- Coalescent simulation and likelihood for phylodynamic inference☆13Updated this week
- Official place for proposals and details around monkeypox virus lineage designations☆20Updated 5 months ago
- R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2☆13Updated 2 months ago
- Scalable relaxed clock phylogenetic dating☆24Updated 5 months ago
- An Amazing Shiny App☆17Updated 3 years ago
- ☆9Updated last year
- A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.☆12Updated 10 months ago
- An R-wrapper for lsd2☆9Updated last year
- Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.☆10Updated 2 years ago
- Analysis of global migration patterns of seasonal influenza viruses☆21Updated 5 years ago
- R package: Evolutionary biology in R☆14Updated 4 months ago
- R package to run BEAST2☆10Updated 2 weeks ago
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆14Updated 4 months ago
- ☆17Updated 4 months ago
- Racmacs R package for performing antigenic cartography☆20Updated 2 months ago
- Disease outbreak reconstruction from epidemiological and genetic data☆30Updated 2 years ago
- Access sequences from the 1000 Plant Initiative (1KP)☆12Updated last year
- Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution.…☆17Updated 6 months ago
- Calculate distances between phylogenetic trees in R☆28Updated last week
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Updated 11 years ago
- An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data☆17Updated 7 months ago
- ☆17Updated 2 years ago
- babette is an R package to work with BEAST2☆44Updated 2 months ago
- ☆14Updated 10 months ago
- Informatic Sequence Classification Trees☆14Updated 3 years ago