Total Functional Score of Enhancer Elements (TFSEE) 

A computational pipeline that integrates data from GRO-seq, RNA-seq, histone modification ChIP-seq (i.e., H3K27ac and H3K4me1),and motif searches, allowing for the simultaneous identification of active enhancers and their cognate transcription factors across many samples. TFSEE integrates (1) the location and magnitude of enhancer activity based on enhancer transcription (GRO-seq); (2) the enrichment of enhancer-related histone modifications (ChIP-seq); (3) the level of TF expression (RNA-seq); (4) the level of target gene expression (RNA-seq); and (5) the TF motif scores for each enhancer. 

groHMM 

A computational tool for analyzing GRO-seq data and identifying unannotated and cell type-specific transcription units from global run-on sequencing data.

Homer

A software package for analyzing GRO-seq data and other types of NGS data sets such as RNA-seq and ChIP-seq

Figure from Chae M. et al (2015) groHMM software. BMC Bioinformatics 

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