delocalizer

streammd

Single-pass probabilistic duplicate marking of alignments with a Bloom filter.

beacon_v2_test_data

Beacon v2 format data from a publicly available dataset

mumbai

Faster position-based slice or lookup on multiple bams

qasim

Simulate mutations, fragment generation and paired-end HTS reads on diploid genomes

adamajava

cromwell

Workflow Execution Engine using WDL

Empire

JPA implementation for RDF

pbspy

Lightweight PBS job submission and monitoring

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

beacon-v2-Models

Models that leverage the Beacon Framework v2

beacon2_data_validator

Validate JSON data files against the beacon v2 data model.

bioconda-recipes

Conda recipes for the bioconda channel.

cpython

The Python programming language

cutstash

Store trimmed adapters in FASTQ sequence id description.

ega-download-client

A basic Python-based EGA download client

ega_metadata

An incomplete set of subpackages of the private `graflipy` package, for instructional purposes only

htsjdk

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

nextflow-s3fs

An S3 File System Provider for Java 7

pbspro

An HPC workload manager and job scheduler for desktops, clusters, and clouds.

pinto

Pinto: A lightweight framework for mapping Java Beans into RDF and back again

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

python-novice-gapminder

Introduction to Python for non-programmers using gapminder data

quip_classification

r-novice-gapminder

Introduction to R for non-programmers using gapminder data.

rdflib

RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

styles

Official repository for Citation Style Language (CSL) citation styles.

tutorial

Code review tutorial exercises

velocyto.py

RNA velocity estimation in Python

Vigelint

A pipeline for determining how the number of variants in clinically significant genes change over time

xmlschema

XML Schema validator and data conversion library for Python