Discover sdwfrost/hernan-robins-julia-code Open Source project

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Julia
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Julia programs for Hernan and Robins' Causal Inference book http://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/

Gillespie.jl

Stochastic Gillespie-type simulations using Julia

Jupyter Notebook

liblsoda

The LSODA algorithm for differential equations as a shared library

phylowidget

An R htmlwidgets package of phylotree.js

HTML

mevr-course-2016

Molecular Epidemiology of Viruses in R

gbmunge

Munge GenBank files into FASTA and tab-separated metadata

epiwidgets

A collection of htmlwidgets handy for epidemiology, etc.

JavaScript

nim-shared-object-example

A simple shared object / dlopen example in nim

Nim

libtn93

C library to compute Tamura-Nei distances between (nucleotide) strings

distributions

Random numbers and distributions for Nim

Nim

nim-plotly-example

Example of using Plotly.js in Nim

JavaScript

nexthiv

Processing code for nextHIV

Python

model-runner-zoo

Examples of models plus connectors for the model runner

Python

biobash

A collection of bash scripts for bioinformatics

Shell

pangea

PANGEA-HIV analyses

Perl

ebov-methods-comparison

Comparison of different molecular clock methods, applied to the West African Ebola epidemic

Jupyter Notebook

eid_presentation

An undergraduate lecture on emerging infectious diseases, written using Reveal.js

JavaScript

mers-treedater

Example of using treedater on MERS-CoV data from Dudas et al. (2017)

HTML

agentscripter

An htmlwidgets package allowing incorporation of Agentscript models into R Markdown documents

HTML

igh-evaluation

Datasets and results to evaluate methods for analysing immunoglobulin sequences

HTML

ptii-bioinformatics

Notes for 2017 Part II CompSci Bioinformatics Algorithms

kemri-phylodynamics

Half day phylodynamics workshop at KEMRI

HTML

mevr-course-ghana

MEVR course resources for University of Ghana 2017

mers-analysis

Phylodynamics in R, applied to MERS Coronavirus

HTML

pangea-trees

Tree comparison exercise for PANGEA-HIV

HTML

igblast-docker

Dockerfile for IgBLAST

bio

All-purpose bioinformatics container

Dockerfile

pipelign

A pipelign for automated multiple sequence alignment

Python

cepi

Simula-style stochastic simulations in C

sparNA

Consensus assembly of deep sequenced RNA virus populations

Python

linear-algebra

linear-algebra.js bundled up

JavaScript

pangea-round2

PANGEA-HIV analyses, round 2

Perl

phylopractical

Shiny App for Part II Pathology Practical

mathmodels.js

A little library of mathematical models in Javascript

HTML

liblsd

A refactoring of least squares dating for use as a library

C++

hiv-antigenic-cartography

Antigenic cartography of HIV using Bayesian multidimensional scaling

mfo23

Talk for Oberwolfach 2023

mevr

Molecular epidemiology of viruses in R

sdwfrost/hernan-robins-julia-code

sdwfrost

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