ENCODE DCC's repositories
chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seq
dna-me-pipeline
DCC/DAC methylation pipeline source
dnase_pipeline
ENCODE DNase-seq pipeline essentials for running on dnanexus.
WranglerScripts
Collection of scripts used by the wranglers to interact with the servers
pipeline-container
Containerization infrastructure for ENCODE analysis pipelines
atac-seq-pipeline-test-data
Test data for ENCODE atac-seq-pipeline
file-validation-pipeline
ENCODE / DNA nexus pipeline for file validation
open-data-registry
A registry of publicly available datasets on AWS
chip-seq-pipeline-test-data
Test data for ENCODE chip-seq-pipeline
genomelake
Simple and efficient access to genomic data for deep learning models.
graphlib
A directed multi-graph library for JavaScript
kentUtils_bin_v377
kentUtils_bin_v377
kentutils_v385_bin_bulkrna
kentutils binaries used by bulkrna
pipeline-utils
ENCODE pipeline utilities
pipeline_accessioning
Accessioning of pipeline data to ENCODE Portal
pre_commit_zipper
Pre commit hook that builds a zip of imports for dnase
pyramid_retry
An execution policy for pyramid that handles retryable errors.
rnaget_service
POC implementation of GA4GH rnaget API
sample_swaps
Explore Sample Swaps from Shoresh paper
stampipes
This is a focused collection of makefiles and scripts for analysis on Illumina sample data.
stanford-intern-2019
My project for my 2019 Stanford summer internship
transcript_id_to_gene_type_mapping
The code and files used to create the mapping from transcript ids to gene types for QC in rna-seq-pipeline.
wdl-pipelines
Documentation for WDL pipelines at ENCODE-DCC