Pinned Repositories
artic-live
Nextstrain data, pipelines, and visualizations for novel pathogen outbreak as part of ARTIC-network live workshop
augur
Pipeline components for real-time virus analysis
British-COVID19-Cluster
Data relating to publication of a case report on the UK/France/Spain COVID-19 cluster in early 2020
cluster-picker-and-cluster-matcher
For all your cluster needs
cov
Coronavirus builds
dengue-antigenic-dynamics
Dengue antigenic variation and evolutionary dynamics
ncov_2021
ncov_cluster
Nextstrain build for novel coronavirus SARS-CoV-2
sarscov2-tutorial
Template & tutorial for SARS-CoV-2 analysis
south-usa-sarscov2
Runs from Southern USA States of SARSCoV2 data
emmahodcroft's Repositories
emmahodcroft/cluster-picker-and-cluster-matcher
For all your cluster needs
emmahodcroft/ncov_cluster
Nextstrain build for novel coronavirus SARS-CoV-2
emmahodcroft/British-COVID19-Cluster
Data relating to publication of a case report on the UK/France/Spain COVID-19 cluster in early 2020
emmahodcroft/south-usa-sarscov2
Runs from Southern USA States of SARSCoV2 data
emmahodcroft/cov
Coronavirus builds
emmahodcroft/sarscov2-tutorial
Template & tutorial for SARS-CoV-2 analysis
emmahodcroft/ncov_2021
emmahodcroft/artic-live
Nextstrain data, pipelines, and visualizations for novel pathogen outbreak as part of ARTIC-network live workshop
emmahodcroft/dengue-antigenic-dynamics
Dengue antigenic variation and evolutionary dynamics
emmahodcroft/echo30
emmahodcroft/enterovirus
To temporarily display enterovirus builds
emmahodcroft/enterovirus_genome
Nextstrain run for full-genome enterovirus
emmahodcroft/sc2_rk_public
Code and scripts used in SARS-CoV-2 R & k analysis
emmahodcroft/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
emmahodcroft/asmngs20
ASMNGS20 - 2020 Conference Details
emmahodcroft/augurlinos
A collection of modules for molecular epidemiology
emmahodcroft/COVID-19_Testing
An open letter on increased testing for COVID-19 in Switzerland
emmahodcroft/emmahodcroft.github.io
GitHub Page
emmahodcroft/enterovirus_vp1
Enterovirus D68 VP1 Nextstrain Analysis
emmahodcroft/ev_d68_enpen2022
Enterovirus-D68 phylogenetic analyses code - actively maintained
emmahodcroft/GC
grand challenges outbreak virus
emmahodcroft/hello-world
GitHub tutorial
emmahodcroft/Intros-CH-AlphaDelta
Code used for the phylogenetic analysis of importations of Alpha and Delta SC2 into Switzerland
emmahodcroft/RVF
emmahodcroft/slate
Slate is a Jekyll theme for GitHub Pages
emmahodcroft/static
Static content about / docs / tutorial / blog posts
emmahodcroft/SVVC
simple viral variant caller
emmahodcroft/tb
TB runs with nextstrain-augur
emmahodcroft/TB-example
Trial TB data for Nextstrain tutorials
emmahodcroft/tbtmr2
Global TB run