ENCODE
Search the ENCODE Portal ENCODE SCREEN Functional genomics Functional characterization Encyclopedia of elements Rush Alzheimer’s EN-TEx Deeply profiled cell lines Protein knockdown …
Data – ENCODE
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ENCORE Matrix – ENCODE
The ENCORE project aims to study protein-RNA interactions by creating a map of RNA binding proteins (RBPs) encoded in the human genome and identifying the RNA elements that the RBPs bind to.
eCLIP Data Standards – ENCODE
Antibodies must be characterized according to standards set by the ENCODE Consortium. Please see the linked documents for transcription factor standards (May 2016), histone modification and …
ENCODE
ENCODE
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 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 , and WGBS.
Histone ChIP-seq Data Standards and Processing Pipeline (ENCODE 4) …
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 proteins that …
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 released to …
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 current …