All software used or developed by the ENCODE Consortium
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REDITs — sourceREDITs contain a suite of tools to identify differential RNA editing sites using RNA-seq data
Software type: other
mountainClimber — sourcemountainClimber is a method for de novo identification of alternative transcript start sites and polyadenylation sites in RNA-seq data
Software type: transcript identification
BEAPR — sourceBEAPR is a method to identify allele-specific binding of RNA-binding proteins using eCLIP-seq data as described in our paper “Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA"
Software type: variant annotation