Discover ENCODE-DCC/dna-nexus-collaboration Open Source project

385

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

UCSC command line bioinformatic utilities

244

kentUtils

167

rna-seq-pipeline

ENCODE Uniform processing pipeline for ChIP-seq

141

chip-seq-pipeline

Metadata database for ENCODE project

120

encoded

JavaScript

110

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

HiC uniform processing pipeline

hic-pipeline

DCC/DAC methylation pipeline source

dna-me-pipeline

Perl

caper

Cromwell/WDL wrapper for Python

ENCODE long read RNA-seq pipeline

long-read-rna-pipeline

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

wgbs-pipeline

mirna-seq-pipeline

The SnoVault general purpose hybrid object-relational database

snovault

Cromwell output organizer

croo

ENCODE DNase-seq pipeline essentials for running on dnanexus.

dnase_pipeline

Shell

demo-pipeline

Uniform analysis pipeline work at UCSC for ENCODE

pyencoded-tools

Jupyter Notebook

encode-data-usage-examples

Jupyter Notebook

uniformAnalysis

Scripts to demonstrate the ENCODE REST API for metadata submission.

submission_sample_scripts

ENCODE DNase-seq pipeline

dnase-seq-pipeline

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

WranglerScripts

DNANexus Whole Genome Bisulphite Analysis Pipeline

Bismark-ENCODE-WGBS

Perl

encValData

AngelScript

encodeOntologies

Python module to download, parse and index ontology files.

Flask based web service providing genomic region search, based on regulomedb.org

genomic-data-service

Module to grab QC metrics from ENCODE uniform processing pipelines

qc_metrics

Python module to upload experiment files and metadata to the ENCODE Portal

accession

geo-submission

Converts multiple QC objects (JSON/TSV/CSV) into a spreadsheet

qc2tsv

Lambda function to compute MD5 hashes of S3 objects

s3-md5-hash

Containerization infrastructure for ENCODE analysis pipelines

pipeline-container

Python code out of the UCSC Genome Brower "kent/src" tree

ucscGb

ENCODE / DNA nexus pipeline for file validation

file-validation-pipeline

segway-pipeline

Hub for data analysis pipelines and software in ENCODE 3.

ENCODE-DAC-pipelines

users-meeting-2020-workshop

atac-seq-pipeline-test-data

Test data for ENCODE atac-seq-pipeline

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

dxencode

snovault-search

ENCODE Imputation Challenge scoring & validation scripts

imputation_challenge

Simple examples of common data and organization types used to vizualize data in the UCSC Genome Browser using Track Hubs

trackhub_example

checkfiles

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.

Repository to try out Django in the implementation of controlled vocabulary and experimental meta-data

cvDjango

WDL pipeline for chromhmm

chromhmm-pipeline

Peformant parallel GET extracted from aws-cli

wgot

Official ENCODE mappings for a variety of terms

Mappings

dccMetadataImport

Tables of metadata to import to the DCC.

encoded-walkme

CSS

modencode

modENCODE temporary site

ptools_bin

Ptools to pypi

Repository for code used in translating encoded metadata to pipelines.

metadata-to-pipelines

regulome-encoded

Temp repo for regulome development

JavaScript

encodemouseportal

A Flask service on Google App Engine to upload files from Google Cloud Storage to AWS S3

gcs-s3-transfer-service

Pipeline to convert bams into pbams

ptools