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Gillespie.jl
Stochastic Gillespie-type simulations using Julialiblsoda
The LSODA algorithm for differential equations as a shared libraryphylowidget
An R htmlwidgets package of phylotree.jsmevr-course-2016
Molecular Epidemiology of Viruses in Rgbmunge
Munge GenBank files into FASTA and tab-separated metadataepiwidgets
A collection of htmlwidgets handy for epidemiology, etc.nim-shared-object-example
A simple shared object / dlopen example in nimdistributions
Random numbers and distributions for Nimnim-plotly-example
Example of using Plotly.js in Nimnexthiv
Processing code for nextHIVmodel-runner-zoo
Examples of models plus connectors for the model runnerbiobash
A collection of bash scripts for bioinformaticshernan-robins-julia-code
Julia programs for Hernan and Robins' Causal Inference book http://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/pangea
PANGEA-HIV analysesebov-methods-comparison
Comparison of different molecular clock methods, applied to the West African Ebola epidemiceid_presentation
An undergraduate lecture on emerging infectious diseases, written using Reveal.jsmers-treedater
Example of using treedater on MERS-CoV data from Dudas et al. (2017)agentscripter
An htmlwidgets package allowing incorporation of Agentscript models into R Markdown documentsigh-evaluation
Datasets and results to evaluate methods for analysing immunoglobulin sequencesptii-bioinformatics
Notes for 2017 Part II CompSci Bioinformatics Algorithmskemri-phylodynamics
Half day phylodynamics workshop at KEMRImevr-course-ghana
MEVR course resources for University of Ghana 2017mers-analysis
Phylodynamics in R, applied to MERS Coronaviruspangea-trees
Tree comparison exercise for PANGEA-HIVigblast-docker
Dockerfile for IgBLASTbio
All-purpose bioinformatics containerpipelign
A pipelign for automated multiple sequence alignmentcepi
Simula-style stochastic simulations in CsparNA
Consensus assembly of deep sequenced RNA virus populationslinear-algebra
linear-algebra.js bundled uppangea-round2
PANGEA-HIV analyses, round 2phylopractical
Shiny App for Part II Pathology Practicalmathmodels.js
A little library of mathematical models in Javascriptliblsd
A refactoring of least squares dating for use as a libraryhiv-antigenic-cartography
Antigenic cartography of HIV using Bayesian multidimensional scalingmfo23
Talk for Oberwolfach 2023mevr
Molecular epidemiology of viruses in RLove Open Source and this site? Check out how you can help us