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adam

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

airr-formats

Open source formats for AIRR data using Thrift.

airr-standards

MiAIRR: AIRR Community Minimal Standards WG

avro

Mirror of Apache Avro

avro2parquet

Hadoop MapReduce tool to convert Avro data files to Parquet format.

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bdg-formats

bdg-utils

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

bedtools2

A powerful toolset for genome arithmetic.

bench-impyla

Benchmarks for impyla

bigdatagenomics.github.io

Web Site for the Big Data Genomics Group

biodata

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics

biojava

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

biopython

Official git repository for Biopython (converted from CVS)

blaze

NumPy and Pandas interface to Big Data

bootstrap

Sleek, intuitive, and powerful front-end framework for faster and easier web development.

bpm

centrifuge

Classifier for metagenomic sequences

clientform

ClientForm python module by John J. Lee

cm_api

Cloudera Manager API Client

common-repo-wg

Recommendations from the AIRR Common Repository Working Group

crunch

Mirror of Apache Crunch (Incubating)

datacache

Helpers for transparently downloading datasets

dataprotocols

Content and specs for dataprotocols.org

deeptcr

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

dotfiles

.files, including ~/.osx — sensible hacker defaults for OS X

dsq

Distributed Streaming Quantiles (for PySpark)

eggo

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

encode_downloader

Downloader for ENCODE

epitopes

tools for epitope mapping