Pinned Repositories
beast-mcmc
Bayesian Evolutionary Analysis Sampling Trees
Delta-analysis
UK-lineage-dynamics-analysis
Large-scale virus genome sequencing reveals the genetic structure and importation dynamics of a national COVID-19 epidemic.
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
figtree.js
Phylogenetic tree library for JavaScript/Node.js
clusterfunk
Miscellaneous tool for phylogenetic clusters
jtmccr1's Repositories
jtmccr1/beast_analysis
A nextflow pipeline to help manage multiple beast MCMC runs
jtmccr1/bft-nf
jtmccr1/CoVEME-tutorial
tutorial adapted from http://beast.community/thorney_beast
jtmccr1/fertree
command line tree manipulation for phylogenetic analysis in rust
jtmccr1/IntroductionToPhylogenetics
jtmccr1/jtmccr1.github.io
jtmccr1/nf-core-phylofunk
An nf-core compatible pipeline for running BEAST analysis
jtmccr1/outbreak.js
a small javascript class for simulating outbreaks
jtmccr1/revealjs-talk
jtmccr1/sampler
tools for subsetting
jtmccr1/sequencing_quality
jtmccr1/Classes
Course work codes and related!
jtmccr1/cookiecutter-data-science
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
jtmccr1/DANG_5_31_2016
A brief introduction to Shiny and interactive figures
jtmccr1/estimate-number-of-transmission
jtmccr1/figtree.js
Phylogenetic tree library for JavaScript/Node.js
jtmccr1/figtreejs-react
jtmccr1/funnel
Funnel is a toolkit for distributed task execution via a simple, standard API.
jtmccr1/HIVEr
R Package for functions commonly used in the HIVE analysis
jtmccr1/kimuraDiffusionPlugin
A plugin for BEAST that estimates Ne from allele trajectories
jtmccr1/lineages
Resources for a lineage naming scheme for SARS-CoV-2/hCoV-2019
jtmccr1/microbialinformatics.github.io
Website for MICRBIOL 612: Microbial Informatics
jtmccr1/parallel-evolution
jtmccr1/sars2
jtmccr1/sequencing_coverage
jtmccr1/skybricks
a beast plugin for a flexible sky* coalescent model api
jtmccr1/transmission-simulator
playing with simulations - *In progress*
jtmccr1/TransPhylo
Reconstruction of transmission trees using genomic data
jtmccr1/trapper
jtmccr1/variant_pipeline
Work on the variant_pipeline and initial r analysis used in calling variants from NGS data