Pinned Repositories
adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
battleship
Board games for my daughter
bigwig4j
A BigWig Reader, in Java
data-use-ontology
A simple ontology for representing data use and research purpose constraints.
datamining-36-350-homework
Source Code for Fall 2009 36-350 Homework
djeocoder
A standalone geocoder, derived from the OpenBlock use of GeoDjango.
ideals
Experimentation with computer algebra in Java
java-obo
Java library for parsing and handling OBO ontologies.
musee
Dynamic web app 'presentations', driven by user scrolling, inspired by the NYT
rasch-model
Implementation of a Rasch Model
tdanford's Repositories
tdanford/musee
Dynamic web app 'presentations', driven by user scrolling, inspired by the NYT
tdanford/pyplans
tdanford/adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
tdanford/battleship
Board games for my daughter
tdanford/ideals
Experimentation with computer algebra in Java
tdanford/ala-coding-class
tdanford/avocado
A Variant Caller, Distributed
tdanford/awa-scraper
tdanford/bdg-formats
Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
tdanford/bdg-services
Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster. Apache 2 licensed.
tdanford/bdg-utils
General (non-omics) code used across BDG products. Apache 2 licensed.
tdanford/bioinfo-algorithms
Experimentation
tdanford/cnv
CNV calling functions and scripts
tdanford/ContEst
Spark implementation of the ContEST contamination estimation algorithm.
tdanford/docs
My writings.
tdanford/dotfiles
Colourful & robust OS X configuration files and utilities.
tdanford/dropwizard-configurable-assets-bundle
An implementation of an AssetBundle for use in Dropwizard that allows user configuration.
tdanford/ga4gh-flask-api
Flask implementation of part of the GA4GH WS API
tdanford/load_tools
Tools for efficient and error-tolerant loading of data into SciDB
tdanford/luigi-workflows
tdanford/metamodel_extras
Extra pluggable modules for Apache MetaModel (but licensed with LGPL)
tdanford/nci_design
tdanford/pybard
tdanford/qc-metrics
Read and variant metrics, useable for pipeline quality control purposes
tdanford/RNAdam
An RNA fusion transcript pipeline built on top of ADAM. Apache 2 licensed.
tdanford/spark-template
A template for projects using Spark, Avro, and Parquet.
tdanford/tdanford.github.io
tdanford/treasure-hunt
Utilities for creating coded treasure hunts for my kids
tdanford/vcf_loader
Prototype loader for the Variant Call Format files
tdanford/vcfc
An experimental VCF flattener in C