Michael L Heuer

Login: heuermh

Company: UC Berkeley AMPLab

Location: Minneapolis, MN USA

Bio: null

Blog: http://www.dishevelled.org

Blog: http://www.dishevelled.org

Member of

1. AMPLab at UC Berkeley
2. BD2K Center for Translational Genomics
3. Big Data Genomics
4. BioJava
5. National Resource for Network Biology
6. piccolo2d

Repositories

adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

adam-commands

External commands in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

adam-dishevelled-bio

dishevelled-bio on Spark via ADAM pipe APIs

adam-examples

Examples in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

adam-pheno

Phenotypes for ADAM: Genomic Data System. Apache 2 licensed.

adam-plugins

External plugins in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

adam-snpeff

SnpEff on Spark via ADAM pipe APIs

avocado

A Variant Caller, Distributed. Apache 2 licensed.

awesome-adam

Awesome list of applications that extend Big Data Genomics ADAM. CC0 licensed.

awesome-adam

Awesome list of applications that extend Big Data Genomics ADAM. CC0 licensed.

awesome-nextflow

A curated list of nextflow based pipelines

basespace-java-sdk

null

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio_validation_workflows

bcbio CWL and WDL validation workflows

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bdg-convert

Conversions to and from Big Data Genomics Avro Formats

bdg-convert-ga4gh

Conversions between GA4GH Protobuf and Big Data Genomics Avro Formats. Apache 2 licensed.

bdg-docs

My writings.

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

bdg-nextflow

Workflows implemented via Nextflow.

bdg-recipes

Recipes using BDG projects. Apache 2 licensed.

bdg-rice

An RNA pipeline built on top of ADAM. Apache 2 licensed.

bdg-rice

An RNA pipeline built on top of ADAM. Apache 2 licensed.

bdg-services

Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster.

bdg-site

Web Site for the Big Data Genomics Group

bdg-utils

General (non-omics) code used across BDG products. Apache 2 licensed.

bioconda-recipes

Conda recipes for the bioconda channel.

biojava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data.

biojava-adam

BioJava and ADAM integration.

biojava-bosc2016

BioJava project BOSC 2016 abstract

biojava.github.io

For now experimental. The potential new hosting of the BioJava homepage.

biojava-http

HTML/JS based user interfaces for BioJava

biojava-legacy

Legacy BioJava 1 Code

biojava-legacy-adam

BioJava 1.x (biojava-legacy) and ADAM integration.

blend4j

blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

brew-apache-spark-switcher

Apache Spark Homebrew switch script

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cannoli

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

cbioportal

null

cgl-docker-lib

null

chuck

ChucK Music Programming Language

chuck-mode

ChucK emacs mode

chugins

Repository for ChuGins

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.

contAdamination

Hacking away on bloom filters and adam...

cytoscape-api

Cytoscape 3 API bundles.

cytoscape-impl

Cytoscape 3 implementation bundles.

data-consumer-vignettes

Simple walk-throughs of interacting with the DCP as a downstream data consumer.

deprecated-homebrew-science

Scientific formulae for the Homebrew package manager

dishevelled

dishevelled.org

dishevelled-bio

dishevelled.org bio

docker-chuck

Docker images for ChucK and related libraries.

docker-flow

Docker container for flow.

docker-linuxbrew-bio

Docker images of bioinformatics software built with Linuxbrew

eggo

Ready-to-go Parquet-formatted public 'omics datasets

ensembl-rest-client

Java client for the Ensembl REST API.

Euclidean-Pattern-Generator

MIDI pattern generator in Java. Generates rhythmic patterns based on the Euclidean algorithm.

executor-processing

Executor library for Processing

findbugs-guice

Findbugs detectors for Guice

flow

Consensus assembly, variant calling, and allele interpretation workflow.

frames-processing

Frames animation library for Processing

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

ga4gh-schemas

Work on data models and APIs for Genomic data.

galaxy-bootstrap

A simple Java package for downloading and configuring Galaxy. Initial work is a framework to test blend4j.

gamepad-processing

Gamepad library for Processing.

gatk

GATK4 development

gemini

a lightweight db framework for disease and population genetics.

genotype-list

Automatically exported from code.google.com/p/genotype-list

gfa-adam

Graphical Fragment Assembly (GFA) 2.0 support for ADAM.

GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

github-changes-maven-plugin

Maven changes plugin for GitHub hosted repositories.

gnocchi

null

googlegenomics-api-client-java

null

googlegenomics-api-provider-local-java

Implements the Google Genomics API locally, reading its data from local BAM files.

googlegenomics-mapreduce-java

Uses the Java MapReduce for Google App Engine to create a variant similarity matrix and run PCA.

googlegenomics-protobufs

Protobuf files used to represent data in the Google Genomics APIs.

Hadoop-BAM

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.

hca-data-store-client

null

heuerandsons.github.io

Heuer and Sons

histogram

Streaming Histograms for Clojure/Java

HlaTools

A series of tools and pipelines for genotyping MHC / HLA genes and alleles using SMRT Sequencing

hml

null

homebrew

The missing package manager for OS X.

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers

homebrew-cbl

Homebrew repository for CloudBioLinux: incubator for formulas to end up in homebrew-science

homebrew-science

Scientific formulae for the Homebrew and Linuxbrew package managers

homebrew-versions

:1234: Versioned formulae for the Homebrew package manager

hook

The longshoreman's hook was historically used by longshoremen (stevedores).

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

ImmunogeneticDataTools

Immunogenetic Data Tools related to HLA, GLStrings, Linkage Disequilibrium

incubator-parquet-mr

Mirror of Apache Parquet

ISAconfigurator

The ISAconfigurator allows for creation of XML files (configuration files) used to build spreadsheets in the ISAcreator and for validation in the creator and ISAvalidation code. Led by Eamonn Maguire, Philippe Rocca-Serra (Uni. of Oxford).

ISAcreator

ISAcreator is a Java desktop application which allows for creation and editing of ISATab files. Led by Eamonn Maguire, Alejandra Gonzalez-Beltran and Philippe Rocca-Serra (Uni. of Oxford).

ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools

java-gcon

Genome connector APIs

jdeb

This library provides an Ant task and a Maven plugin to create Debian packages from Java builds in a truly cross platform manner.

leap-motion-processing

Leap Motion library for Processing

libchuck

ChucK Library Module

libpd

Turning Pure Data into an embeddable audio synthesis library

lick

LiCK, Library for ChucK

lick-ios

iOS app template with libchuck and LiCK

lime

Distributed Set Theory for Genomics

mango

A scalable genome browser. Apache 2 licensed.

midi-looper

MIDI looper library for Processing.

monome-emulator

Monome emulator written in Processing.

nameless

Nameless

nextflow

A DSL for data-driven computational pipelines

ngs

null

osc-looper

OSC looper library for Processing.

Parallel-Bitset-Operations

Boosts Lucene searchers that heavily use bitsets

personal-genome-client

Java client for the 23andMe Personal Genome API.

phenopacket-format

null

phenopacket-protobuf

Protobuf support for phenopackets

phenopacket-reference-implementation

Reference java implementation for phenopackets

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

piccolo2d.java

Structured 2D Graphics Framework

piccolo2d-processing

Piccolo2D library for Processing.

projects

a list of all projects

puredatap5

Tentative Processing support for libpd; use at your own risk.

quinine

Read and variant metrics, useable for pipeline quality control purposes. Apache 2 licensed.

Rack

Open-source virtual Eurorack DAW

bdg-rice

An RNA pipeline built on top of ADAM. Apache 2 licensed.

bdg-rice

An RNA pipeline built on top of ADAM. Apache 2 licensed.

rwmidi

midi library for processing.org / java

service-common

Services common libraries.

service-epitope

T-cell epitope group matching service for DPB1 locus

service-feature

Enumerated sequence feature service.

service-hml

HML service

service-parent

Services parent pom.

SnpEff

null

spark

Mirror of Apache Spark

spark-1

A Sinatra inspired framework for java

SparkAdamTest

null

sparkling

Hard fork of perwendel/spark

spark-template

Template routes for Spark web framework

spark-website

Mirror of Apache Spark Website

SpinCAD-Designer

SpinCAD Designer is an open source Java project which allows creation of patches for the Spin FV-1 audio DSP chip.

themidibus

A simple MIDI Library for Processing

toil-scripts

A collection of scripts that use Toil to implement genomics pipelines

UTC-0500

null

VariantDB_Challenge

Finding a scalable alternative to the VCF File for genomics analysis

variation-cytoscape3-app

Git mirror of dishevelled.org variation-cytoscape3-app

vcf_spec

Specification document for the Variant Call Format

velocity-cli

Command line interface to Apache Velocity.

venneuler

Source mirror of unreleased venneuler artifact.

wire

Clean, lightweight protocol buffers for Android and Java.

workflows

Toil workflows for bigdatagenomics tools. Apache 2 licensed.

Commits To