jtmccr1

beast_analysis

A nextflow pipeline to help manage multiple beast MCMC runs

bft-nf

CoVEME-tutorial

tutorial adapted from http://beast.community/thorney_beast

fertree

command line tree manipulation for phylogenetic analysis in rust

GF_analysis

The analysis of the GF colonization experiments

IntroductionToPhylogenetics

jtmccr1.github.io

nf-core-phylofunk

An nf-core compatible pipeline for running BEAST analysis

outbreak.js

a small javascript class for simulating outbreaks

revealjs-talk

sampler

tools for subsetting

sequencing_quality

Classes

Course work codes and related!

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

DANG_5_31_2016

A brief introduction to Shiny and interactive figures

estimate-number-of-transmission

figtreejs-react

funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

HIVEr

R Package for functions commonly used in the HIVE analysis

kimuraDiffusionPlugin

A plugin for BEAST that estimates Ne from allele trajectories

lineages

Resources for a lineage naming scheme for SARS-CoV-2/hCoV-2019

microbialinformatics.github.io

Website for MICRBIOL 612: Microbial Informatics

parallel-evolution

sars2

sequencing_coverage

skybricks

a beast plugin for a flexible sky* coalescent model api

transmission-simulator

playing with simulations - *In progress*

TransPhylo

Reconstruction of transmission trees using genomic data

trapper

variant_pipeline

Work on the variant_pipeline and initial r analysis used in calling variants from NGS data