ENCODE Software
All software used or developed by the ENCODE Consortium
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- CRADLE — sourceCRADLE (Correcting Read counts and Analysis of DifferentiaLly Expressed regions) is a package that was developed to analyze STARR-seq data. CRADLE removes technical biases from sonication, PCR, mappability and G-quadruplex sturcture, and generates bigwig files with corrected read counts. CRADLE then uses those corrected read counts and detects both activated and repressed enhancers. CRADLE will help find enhancers with better accuracy and credibility.
- windowTrimmer — sourceThis script is intended to crawl through bed files to filter out reads that are too concentrated within a specified base-pair window.