encode-project.yaml

Name: Encyclopedia of DNA Elements (ENCODE)
Description: |
  The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of
  research groups funded by the National Human Genome Research Institute (NHGRI). The goal
  of ENCODE is to build a comprehensive parts list of functional elements in the human genome,
  including elements that act at the protein and RNA levels, and regulatory elements that
  control cells and circumstances in which a gene is active. ENCODE investigators employ a
  variety of assays and methods to identify functional elements. The discovery and annotation
  of gene elements is accomplished primarily by sequencing a diverse range of RNA sources,
  comparative genomics, integrative bioinformatic methods, and human curation. Regulatory
  elements are typically investigated through DNA hypersensitivity assays, assays of
  DNA methylation, and immunoprecipitation (IP) of proteins that interact with DNA and RNA,
  i.e., modified histones, transcription factors, chromatin regulators, and
  RNA-binding proteins, followed by sequencing.
Contact: encode-help@lists.stanford.edu
ManagedBy: ENCODE Data Coordinating Center
Documentation: https://www.encodeproject.org
UpdateFrequency: Daily
Tags:
  - aws-pds
  - biology
  - bioinformatics
  - genetic
  - genomic
  - life sciences
  - machine learning
  - deep learning
License: External data users may freely download, analyze, and publish results based on any ENCODE data without restrictions.
Resources:
  - Description: Released and archived ENCODE data
    ARN: arn:aws:s3:::encode-public
    Region: us-west-2
    Type: S3 Bucket
DataAtWork:
  Tutorials:
    - Title: Exploring ENCODE data from EC2 with Jupyter notebook
      URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/mount_s3_bucket_and_run_jupyter_on_ec2.ipynb
      AuthorName: Keenan Graham
      AuthorURL: https://github.com/keenangraham
    - Title: ENCODE CTCF ChIP-seq data correlation across different cell types
      URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/ctcf_chip_seq_cross_cell_type_correlation.ipynb
      AuthorName: Paul Sud
      AuthorURL: https://github.com/p-sud
    - Title: Ingesting ENCODE data into TileDB with S3 backend
      URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/ingest_encode_data_tile_db_with_s3_backend.ipynb
      AuthorName: Otto Jolanki
      AuthorURL: https://github.com/ottojolanki
  Tools & Applications:
  Publications: