ENCODE DCC

Metadata database for ENCODE project

The SnoVault general purpose hybrid object-relational database

ENCODE ATAC-seq pipeline

HiC uniform processing pipeline

An infrastructure to run gemBS pipeline https://github.com/heathsc/gemBS

ENCODE Uniform processing pipeline for ChIP-seq

Documentation for WDL pipelines at ENCODE-DCC

Files are checked to see if the MD5 sum (both for gzipped and ungzipped) is identical to the submitted metadata, as well as run through the validateFiles program from jksrc.

Test data for ENCODE chip-seq-pipeline

Test data for ENCODE atac-seq-pipeline

Utility module to interface encoded metadatabase, AWS, and DNANexus api for Universal Pipelines

Collection of scripts used by the wranglers to interact with the servers

ENCODE DNase-seq pipeline essentials for running on dnanexus.

ENCODE / DNA nexus pipeline for file validation

UCSC command line bioinformatic utilities

Containerization infrastructure for ENCODE analysis pipelines

STAR based ENCODE Long RNA-Seq processing pipeline

Fork of weighted tree from vizuly

DCC/DAC methylation pipeline source

Support files for GA4GH/DREAM workflow challenge

ENCODE analysis pipelines Docker images

ENCODE analysis pipelines cwl scripts

temporary test-github-integration-repo