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hmp2lims

Project 3: Prediabetes Type 2 diabetes mellitus (T2D) is a significant health problem facing our nation. Close to 20 million individuals in the United States have T2D, and 79 million aged 20 years or older are clinically pre-diabetic, with a 5-year conversion rate of 10% to 23% from prediabetes to T2D. In a collaborative effort to systematically understand diabetes and its etiology, the team is comprised of leading experts in research on both the human host as well as the microbiome, as properties of both are likely relevant in T2D development. For a better elucidation of mechanisms of onset and progression of T2D disease, the group is performing a detailed analysis of the biological processes that occur in the microbiome and human host by longitudinal profiling of patients at risk for T2D. Both microbiome and host profiles are being analyzed by state-of-the-art omics platforms, and these large-scale and diverse data sets will be integrated to determine the dynamic pathways that change during the onset and progression of T2D, especially during viral infections and other stresses. This longitudinal study is expected to reveal changes in the microbiome and host at an unprecedented level of detail, and identify molecules and pathways that play important roles in diabetes onset and progression.

htan

hubmap

hugeseq

For original Nature Biotechnology Publication (Q1 2012)

hummingbird

Hummingbird: Efficient Performance Prediction for Executing Genomic Applications in the Cloud: https://doi.org/10.1093/bioinformatics/btab161

illumina_fastq

Tools for parsing Illumina FASTQ files. You can create a barcode distribution of unmatched reads, and extract barcodes of interest.

ingenuity-util

A command-line utility to upload VCF's using the Ingenuity Datastream API.

iris

A bird's-eye view of variant annotations.

jsonwf

A JSON workflow framework

koalatea

Quality control pipeline

loom

A tool for running bioinformatics workflows locally or in the cloud.

loom-workflows

mvp-on-gcp

Tools used to process MVP data on Google Cloud Platform

mvp_aaa_codelabs

Queries to perform qc and analysis on genomes in BigQuery

personal-health-dashboard

phd-website

pipelines-api-examples

Examples for the Google Genomics Pipelines API.

pizza

playground

For testing and learning git

practices

pubble

pulsarpy

The official Python client for Pulsar LIMS

pulsarpy-to-encodedcc

Client for submitting experiments in Pulsar LIMS to the ENCODE Portal https://pulsarpy-to-encodedcc.readthedocs.io/en/latest/dcc_submit.html

pulsarpy_dx

A client for Pulsar LIMS that integrates sequencing results from DNAnexus: https://pulsarpy-dx.readthedocs.io/en/latest/

pulsar_lims

A LIMS for ENCODE submitting labs.

qualia

Scripts for preparation and processing of exome data from Claritas

rsem_utils

scdecode

scgpm-wearables

An iOS app for letting users enter notes about current health and travel events. Open with XCode.

scgpm_lims

A python client for the SCGPM LIMS API