ENCODE DCC

atac-seq-pipeline

ENCODE ATAC-seq pipeline

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

rna-seq-pipeline

encoded

Metadata database for ENCODE project

hic-pipeline

HiC uniform processing pipeline

caper

Cromwell/WDL wrapper for Python

long-read-rna-pipeline

ENCODE long read RNA-seq pipeline

wgbs-pipeline

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

mirna-seq-pipeline

snovault

The SnoVault general purpose hybrid object-relational database

pyencoded-tools

dnase-seq-pipeline

ENCODE DNase-seq pipeline

encValData

genomic-data-service

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

accession

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

geo-submission

valis-hpgv

High performance WebGL genome visualization

imputation_challenge

ENCODE Imputation Challenge scoring & validation scripts

segway-pipeline

snovault-search

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.

d3-sequence-logo

Sequence Logo generation in d3.js

regulome-encoded

Temp repo for regulome development

autouri

Recursive localization for various types of URIs

coalesce_s3_log_glue_spark

Glue pyspark job to combine s3 access logs to parquet

correlation_robustness

filemetadata_dynamoDB

Load selected encode file metadata to dynamoDB

google-sheet-metadata-submitter

ENCODE metadata submitter based on Google Sheet and Apps script

ihec-processing

IHEC processing

kentUtils_bin_v381

kentUtils_bin_v381 (binary from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)