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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 nimlibtn93
C library to compute Tamura-Nei distances between (nucleotide) stringsdistributions
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 librarymfo23
Talk for Oberwolfach 2023mevr
Molecular epidemiology of viruses in RLove Open Source and this site? Check out how you can help us