ENCODE
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ENCODE Encyclopedia, Version 4: Genomic annotations – ENCODE
The ENCODE Consortium not only produces high-quality data, but also analyzes the data in an integrative fashion. The ENCODE Encyclopedia organizes the most salient analysis products into annotations and provides tools to search and visualize them.
Search – ENCODE
Lab: Erez Aiden, Baylor Project: ENCODE Treatments: 30 ng/mL Interleukin-12 subunit beta (UniProtKB:P29460) for 36 hours, 30 ng/mL Interleukin-12 subunit alpha (UniProtKB:P29459) …
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 that control cells and circumstances in which a gene is active.
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 stages from 10.5 days after conception until birth, including …
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 the web can be used as programmatic queries.
Data – ENCODE
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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 chromatin-associated protein standards (October 2016), and RNA binding protein standards (November 2016).
Whole-Genome Bisulfite Sequencing Data Standards and
The WGBS pipeline was developed as a part of the ENCODE Uniform Processing Pipelines series 1. The full WGBS pipeline code is available on Github and can be run on DNAnexus (link requires account creation) at their current pricing.
Histone ChIP-seq Data Standards and Processing Pipeline - ENCODE
The ENCODE consortium has developed two analysis pipelines to study the different classes of protein-chromatin interactions. Both ChIP-seq piplines share the same mapping steps, but differ in the methods for signal and peak calling and in the subsequent statistical treatment of replicates.