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atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline.

aws-cloudformation-templates

A collection of useful CloudFormation templates

aws-genomics-workflows

T2D AMP Consortium Genomics Workflows on AWS

cellxgene

An interactive explorer for single-cell transcriptomics data

cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

crocpot

CROCPOT is a repository of epigenomic datasets linking distal cis-regulatory elements to their putative target genes including 3D chromatin interactions, single cell co-activity, activity-by-contact (ABC) and CRISPRi regulatory screens.

demultiplex

Pipeline for demultiplexing and doublet detection + checking method robustness

dga-ubuntu-installation

dig-aggregator-methods

Monorepo of methods implemented for the Aggregator

dig-bioindex

BIO index for genetic records stored in S3 and FastAPI server.

dig-loam-stream

dig-loam-stream

expression-profiling-app

The Gene Expression Profiling App displays the snRNA-seq data

igv-react

igv-webapp

IGV Web App

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

kentutils

UCSC command line bioinformatic utilities

lung-epigenome

The goal of this project is to provide data on the genome and epigenome of the human lung to facilitate research efforts of investigators studying diseases of the lung including COVID-19.

pyencoded-tools

Scripts to add and release datasets (based on https://github.com/ENCODE-DCC/pyencoded-tools)

react-annotation-graph

This application links Co-accessibility of distal regulatory variants to putative target genes

rest-api

T2DREAM application programming interface provides developers with a programmatic interface to query and download data

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

snovault

The resource is based on software developed by the ENCODE DCC at Stanford University.

t2dream-portal

The Common Metabolic Disease Genome Atlas (CMDGA) resource is a component of AMP-CMD being developed at the University of California San Diego as part of a larger consortium of academic, industry and non-profit institutions worldwide. The resource is based on software developed by the ENCODE DCC at Stanford University.

variant-nw

Variant Network Visualization Tool. Credit for Dash tool @smorabit