HopkinsIDD / phylosampLinks
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.
☆13Updated 2 years ago
Alternatives and similar repositories for phylosamp
Users that are interested in phylosamp are comparing it to the libraries listed below
Sorting:
- Metagenomics calibration R package☆20Updated 3 years ago
- Estimating time trees from very large phylogenies☆28Updated last year
- R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2☆13Updated 3 weeks ago
- An automated pipeline for retrieving orthologous DNA sequences from GenBank in R☆25Updated 3 months ago
- ☆19Updated 7 months ago
- Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.☆10Updated 3 years ago
- An Amazing Shiny App☆17Updated 4 years ago
- Coalescent simulation and likelihood for phylodynamic inference☆14Updated 6 months ago
- Disease outbreak reconstruction from epidemiological and genetic data☆34Updated last year
- Tools for evolutionary forecasting☆14Updated 2 months ago
- Official place for proposals and details around monkeypox virus lineage designations☆23Updated 2 months ago
- babette is an R package to work with BEAST2☆46Updated last month
- This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://gr…☆16Updated last year
- phylogenetic networks using ggplot2 and ggtree☆13Updated 11 months ago
- Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline f…☆25Updated 2 years ago
- R package to run BEAST2☆11Updated last month
- ☆11Updated 6 months ago
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆14Updated last year
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆40Updated 2 weeks ago
- Calculate distances between phylogenetic trees in R☆34Updated last week
- Fast alignment-free pangenome creation and exploration☆28Updated 5 years ago
- Analysis of global migration patterns of seasonal influenza viruses☆22Updated 6 years ago
- Molecular Epidemiology of Viruses in R☆19Updated 10 years ago
- Snakemake template for building reusable and scalable machine learning pipelines with mikropml☆13Updated 9 months ago
- Informatic Sequence Classification Trees☆15Updated 6 months ago
- A pipeline for extracting SSU rRNA gene from wgs data and applying them for further diversity analysis☆10Updated 9 years ago
- Software for the Tree-Based Scan Statistic☆12Updated last week
- Scalable relaxed clock phylogenetic dating☆27Updated 2 months ago
- Explore spaces of phylogenetic trees☆29Updated 3 months ago
- R package: Evolutionary biology in R☆19Updated last month