huddlej
Staff scientist in @blab at Fred Hutchinson Cancer Center studying predictive models of influenza evolution.
@blab @nextstrain
Pinned Repositories
flu-forecasting
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
popcast
Long-term forecasts for pathogen populations
dms-view.github.io
Interactive visualization of mutational antigenic profiling data
cushion
A Django application for browsing and editing CouchDB documents.
django-csv-admin
Django admin interface for validating and saving uploaded CSV files as form data.
django-wysiwyg-forms
WYSIWYG form editor/creator django app
pnwmoths
augur
Pipeline components for real-time phylodynamic analysis
ncov
Nextstrain build for novel coronavirus SARS-CoV-2
seasonal-flu
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
huddlej's Repositories
huddlej/dotfiles
Personal dot files
huddlej/example-nextstrain-workflow
Example Nextstrain workflow based on public SARS-CoV-2 sequences from GenBank
huddlej/seasonal-flu-reports
huddlej/2019-06-21-ttt-fredhutch
huddlej/architecture-patterns-with-python
Example application code for the python architecture book
huddlej/bioconda-recipes
Conda recipes for the bioconda channel.
huddlej/cartography
Reduced dimension embeddings for pathogen sequences
huddlej/dissertation
PhD dissertation
huddlej/doom.d
doom emacs config files
huddlej/flu_frequencies
huddlej/git-novice
Software Carpentry introduction to Git for novices.
huddlej/huddlej.github.io
huddlej/mobility-on-phylogenies
Minimal example of mapping mobility data to phylogenies of SARS-CoV-2 genomes
huddlej/multifurcating_trees
huddlej/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
huddlej/ncov-africa
Example SARS-CoV-2 build for South Africa
huddlej/ncov-kenya
Example build configuration for SARS-CoV-2 analysis for Kenya
huddlej/nextclade_data_workflows
huddlej/nextstrain-narratives
Demonstration of how to use Nextstrain narratives
huddlej/nextstrain-narratives-demo
Demonstration of Nextstrain narratives
huddlej/planets
huddlej/planets-test
huddlej/santa-sim
A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
huddlej/seasonal-flu-from-ncov
A quick and dirty attempt to implement a seasonal flu pipeline with the existing ncov workflow
huddlej/TreeKnit.jl
TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).
huddlej/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
huddlej/TreeTools.jl
Tools for handling phylogenetic or genealogic trees with Julia. Mainly serves as a dependency for my other package TreeKnit
huddlej/usa-sarscov2
Prototype of state- and territory-level SARS-CoV-2 Nextstrain builds
huddlej/veme-2022
Workshop for VEME 2022
huddlej/zika-tutorial
Data and scripts for Zika virus tutorial