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/pnwmoths
huddlej/msa_classifier
Multiple sequence alignment (MSA) classifier
huddlej/bac_analysis
BAC analysis pipeline(s)
huddlej/behavior-tracker
behavior tracker for fly experiments or any other kind of time-based tracking
huddlej/blasr
This is an unsupported fork of the PacBio blasr aligner. It contains my (very beta) optimizations and new functionality. It may disappear at any time.
huddlej/clone_mapping
Pipeline for generating SUNK pileups from clone sequence data
huddlej/clone_msa_builder
Pipeline for building multiple sequence alignments (MSA) from a database of clones
huddlej/django_lims
A Django-based laboratory information management system
huddlej/django_sims
Sample management inspired by nkrumm's SIMS
huddlej/fasta_tools
Tools for working with FASTA files and related formats
huddlej/fauna
Rethink database to support real-time virus analysis
huddlej/fitbeats
Evolutionary composition of rhythms
huddlej/freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
huddlej/learning_seqan
Code generated while learning SeqAn
huddlej/masters-research-code
code related to my 2012 Masters research
huddlej/MPI_mrsfast_mapping
huddlej/nextflu
Real-time tracking of influenza evolution
huddlej/notebooks
Notebooks to share with others
huddlej/populations
Python module for population genetics
huddlej/pygenome
A library of genomic tools in Python.
huddlej/RD_pipelines
huddlej/safe_projects
Project management with git
huddlej/setup
Reproducible system setup
huddlej/sge_dashboard
A simple dashboard for grid engine
huddlej/snake-cnv
Snakemake-based CNV calling pipeline using MrCaNaVar and mrsFAST
huddlej/suns
Find SUNs for a genome based on its WGAC and SUNK coordinates. Analysis is based on Sudmant et al. 2010 (Science).
huddlej/tab-to-vcf
Convert tab-delimited file into a VCF
huddlej/workshop-2016-cwu
huddlej/workshop-2018-hutch-explorers
Workshop on computational biology with Hutch Explorers
huddlej/workshop-wwu-2016
Website and slides for bioinformatics workshop at WWU