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atac-seq-pipeline
ENCODE ATAC-seq pipelinechip-seq-pipeline2
ENCODE ChIP-seq pipelinekentUtils
UCSC command line bioinformatic utilitiesrna-seq-pipeline
chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seqencoded
Metadata database for ENCODE projectlong-rna-seq-pipeline
STAR based ENCODE Long RNA-Seq processing pipelinehic-pipeline
HiC uniform processing pipelinedna-me-pipeline
DCC/DAC methylation pipeline sourcecaper
Cromwell/WDL wrapper for Pythonlong-read-rna-pipeline
ENCODE long read RNA-seq pipelinewgbs-pipeline
ENCODE whole-genome bisulfite sequencing (WGBS) pipelinemirna-seq-pipeline
snovault
The SnoVault general purpose hybrid object-relational databasecroo
Cromwell output organizerdnase_pipeline
ENCODE DNase-seq pipeline essentials for running on dnanexus.demo-pipeline
pyencoded-tools
encode-data-usage-examples
uniformAnalysis
Uniform analysis pipeline work at UCSC for ENCODEsubmission_sample_scripts
Scripts to demonstrate the ENCODE REST API for metadata submission.dnase-seq-pipeline
ENCODE DNase-seq pipelineWranglerScripts
Collection of scripts used by the wranglers to interact with the serversBismark-ENCODE-WGBS
DNANexus Whole Genome Bisulphite Analysis PipelineencValData
encodeOntologies
Python module to download, parse and index ontology files.genomic-data-service
Flask based web service providing genomic region search, based on regulomedb.orgqc_metrics
Module to grab QC metrics from ENCODE uniform processing pipelinesaccession
Python module to upload experiment files and metadata to the ENCODE Portalgeo-submission
qc2tsv
Converts multiple QC objects (JSON/TSV/CSV) into a spreadsheets3-md5-hash
Lambda function to compute MD5 hashes of S3 objectspipeline-container
Containerization infrastructure for ENCODE analysis pipelinesucscGb
Python code out of the UCSC Genome Brower "kent/src" treefile-validation-pipeline
ENCODE / DNA nexus pipeline for file validationsegway-pipeline
ENCODE-DAC-pipelines
Hub for data analysis pipelines and software in ENCODE 3.users-meeting-2020-workshop
atac-seq-pipeline-test-data
Test data for ENCODE atac-seq-pipelinedxencode
Utility module to interface encoded metadatabase, AWS, and DNANexus api for Universal Pipelinessnovault-search
imputation_challenge
ENCODE Imputation Challenge scoring & validation scriptstrackhub_example
Simple examples of common data and organization types used to vizualize data in the UCSC Genome Browser using Track Hubscheckfiles
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.chromhmm-pipeline
WDL pipeline for chromhmmdna-nexus-collaboration
ENCODE-DNANexus collaborationwgot
Peformant parallel GET extracted from aws-cliMappings
Official ENCODE mappings for a variety of termsdccMetadataImport
Tables of metadata to import to the DCC.encoded-walkme
modencode
modENCODE temporary siteptools_bin
Ptools to pypimetadata-to-pipelines
Repository for code used in translating encoded metadata to pipelines.regulome-encoded
Temp repo for regulome developmentencodemouseportal
gcs-s3-transfer-service
A Flask service on Google App Engine to upload files from Google Cloud Storage to AWS S3ptools
Pipeline to convert bams into pbamsencode_slims
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