huddlej
Staff scientist in @blab at Fred Hutchinson Cancer Center studying predictive models of influenza evolution.
@blab @nextstrain
huddlej's Stars
CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
attractivechaos/klib
A standalone and lightweight C library
pymc-devs/pymc-resources
PyMC educational resources
nextstrain/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
PyTables/PyTables
A Python package to manage extremely large amounts of data
bcbio/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
benbalter/jekyll-auth
A simple way to use GitHub OAuth to serve a protected Jekyll site to your GitHub organization
sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
pezmaster31/bamtools
C++ API & command-line toolkit for working with BAM data
broadgsa/gatk
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
genometools/genometools
GenomeTools genome analysis system.
jtleek/firstpaper
atks/vt
A tool set for short variant discovery in genetic sequence data.
broadinstitute/viral-ngs
Viral genomics analysis pipelines
applied-science/emacs-vega-view
A mode to facilitate interactive data visualization using Vega from within emacs
fhcrc/seqmagick
An imagemagick-like frontend to Biopython SeqIO
command-line-bootcamp/cli-boot.camp
:computer: command-line bootcamp adventure in your browser
zeeev/wham
Structural variant detection and association testing
ngsutils/ngsutils
Tools for next-generation sequencing analysis
sanger/sequencescape
Web based LIMS
brentp/fastahack-python
cython wrapper to fastahack
brentp/bwa-mips
Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit
huddlej/django-csv-admin
Django admin interface for validating and saving uploaded CSV files as form data.
seandavi/SimpleSnakemakeTutorial
ucsc-mus-strain-cactus/comparativeAnnotator
yhwu/sam2psl
Convert SAM format to PSL format
UMCUGenetics/GATK-QScripts
GATK QScripts used in our illumina variant calling pipeline.
huddlej/django-csv-importer
Arbitrary CSV data importer for Django
bbcf/biorepo
BioRepo is a LIMS for HTS data @ EPFL - Vital-IT
tsibley/fastj
Structured metadata for your FASTA sequences.