ENCODE DCC

Pinned Repositories

atac-seq-pipeline
ENCODE ATAC-seq pipeline
Language:Python383 25 313172
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.
Language:Python2 17 00
chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seq
Language:Python120 39 253
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python241 26 175123
encoded
Metadata database for ENCODE project
Language:JavaScript110 31 3351
kentUtils
UCSC command line bioinformatic utilities
Language:C166 45 095
pyencoded-tools
Language:Jupyter Notebook10 32 213
rna-seq-pipeline
Language:Python140 17 4161
snovault
The SnoVault general purpose hybrid object-relational database
Language:Python16 32 228
WranglerScripts
Collection of scripts used by the wranglers to interact with the servers
Language:Python5 25 04

ENCODE DCC's Repositories

ENCODE-DCC/submission_sample_scripts
Scripts to demonstrate the ENCODE REST API for metadata submission.
Language:Python85
ENCODE-DCC/uniformAnalysis
Uniform analysis pipeline work at UCSC for ENCODE
Language:Python8 20 02
ENCODE-DCC/Bismark-ENCODE-WGBS
DNANexus Whole Genome Bisulphite Analysis Pipeline
Language:Perl5
ENCODE-DCC/encodeOntologies
Python module to download, parse and index ontology files.
Language:Python4
ENCODE-DCC/qc_metrics
Module to grab QC metrics from ENCODE uniform processing pipelines
Language:Python3
ENCODE-DCC/cvDjango
Repository to try out Django in the implementation of controlled vocabulary and experimental meta-data
Language:Python2
ENCODE-DCC/ENCODE-DAC-pipelines
Hub for data analysis pipelines and software in ENCODE 3.
2
ENCODE-DCC/ucscGb
Python code out of the UCSC Genome Brower "kent/src" tree
Language:Python2
ENCODE-DCC/dccMetadataImport
Tables of metadata to import to the DCC.
Language:HTML11
ENCODE-DCC/dna-nexus-collaboration
ENCODE-DNANexus collaboration
Language:R11
ENCODE-DCC/encode_slims
1
ENCODE-DCC/encodemouseportal
Language:Python1
ENCODE-DCC/Mappings
Official ENCODE mappings for a variety of terms
1
ENCODE-DCC/Meta-capture-pure-js-prototype
Prototype Metadata capture in JSON using Jade / Bootstrap / Knockout JS / Express / Mongoose
Language:JavaScript1
ENCODE-DCC/modencode
modENCODE temporary site
Language:HTML11
ENCODE-DCC/modENCODE-comparative-website
Comparative modENCODE/ENCODE website.
Language:CSS1
ENCODE-DCC/s3-bucket-listing
Create nice directory listings for s3 buckets with javascript and HTML.
Language:JavaScript1 16 0
ENCODE-DCC/trackhub_example
Simple examples of common data and organization types used to vizualize data in the UCSC Genome Browser using Track Hubs
1
ENCODE-DCC/wgot
Peformant parallel GET extracted from aws-cli
Language:Python1
ENCODE-DCC/DAC_submissions
Scripts to support data and metadata submissions from the DAC
Language:Python
ENCODE-DCC/ENCODE_Data_Hubs
Language:Python
ENCODE-DCC/encoded_commands
Commands installed on mahout
Language:Python
ENCODE-DCC/fetch
A window.fetch JavaScript polyfill.
Language:JavaScript
ENCODE-DCC/GA4GH-DREAM
Support files for GA4GH/DREAM workflow challenge
ENCODE-DCC/pipeline-cwl
ENCODE analysis pipelines cwl scripts
Language:Shell
ENCODE-DCC/pipeline-images
ENCODE analysis pipelines Docker images
Language:Python
ENCODE-DCC/react-bootstrap
Bootstrap 3 components built with React
Language:JavaScript
ENCODE-DCC/temp-test-integration-repo
temporary test-github-integration-repo
ENCODE-DCC/trackhubtest
Regression Test's for UCSC Genome Browser Track Hubs
ENCODE-DCC/weightedtree
Fork of weighted tree from vizuly
Language:JavaScript