ENCODE at UCSC (2003-2012)   -   Downloads   -   Experiment Summary   -   Experiment Matrix   -   ChIP-seq Matrix
ENCODE Project at NHGRI Software Tools Used to Create the ENCODE Resource

Contents

Updated 21 March 2014

Tools for identifying features from ENCODE assays

ChIP-seq Peak Callers


RNA-seq Analysis


Other

Integrative analysis across data types

Genome Segmentation


Other

Quality Metrics for ENCODE data

Other Tools