ENCODE
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Getting Started – ENCODE
Instructions on how to browse and search for ENCODE data programmatically are provided in the REST API help document. In brief, all queries (see Query building) that can be performed via …
Access to ENCODE data
All data generated by the ENCODE consortium is submitted to the DCC and available from the ENCODE portal (http://www.encodeproject.org). The data are reviewed for quality and …
SCREEN: Search Candidate Regulatory Elements by ENCODE
SCREEN is a web interface for searching and visualizing the Registry of candidate cis-Regulatory Elements (cCREs) derived from ENCODE data. The Registry contains 1,063,878 human …
Data Processing Pipelines – ENCODE
The ENCODE Data Coordinating Center has developed data processing pipelines for major assay types generated by the project: RNA-seq, RAMPAGE 1, ChIP-seq, DNase-seq, ATAC-seq 2 , …
publications – ENCODE
The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental …
ATAC-seq Data Standards and Processing Pipeline – ENCODE
The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment.
Data standards – ENCODE
The ENCODE Consortium has adopted shared experimental guidelines for the most common ENCODE assays. The guidelines have evolved over time as technologies have changed, and …
Project Overview – ENCODE
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 …
Histone ChIP-seq Data Standards and Processing Pipeline - ENCODE
The ENCODE consortium has developed two analysis pipelines to study two different classes of protein-chromatin interactions. The histone ChIP-seq pipeline, described here, is suitable for …