Global run-on sequencing data analysis bioinformatics software tools
Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for…
Desktop app
G T A T C G C T A Hypergeometric… Hypergeometric Optimization of Motif EnRichment

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

Desktop app
G T A T C G C T A Fast Read Stitcher Fast Read Stitcher

FStitch Fast Read Stitcher

A fast and simple algorithm to detect nascent RNA transcription in global…

A fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). FStitch takes advantage of two popular machine-learning techniques, a hidden Markov…

Desktop app
G T A T C G C T A groHMM groHMM

groHMM

A package which defines the boundaries of transcription units de novo using a…

A package which defines the boundaries of transcription units de novo using a two state hidden-Markov model (HMM). groHMM is a complete pipeline for the accurate identification of the boundaries of…

Desktop app
G T A T C G C T A Vespucci Vespucci

Vespucci

An algorithm for de novo transcript identification from GRO-sequencing data,…

An algorithm for de novo transcript identification from GRO-sequencing data, along with a system that determines transcript regions, stores them in a relational database and associates them with…

Desktop app
G T A T C G C T A discriminative… discriminative Regulatory-Element detection from…

dREG discriminative Regulatory-Element detection from GRO-seq

A sensitive machine learning method that uses support vector regression to…

A sensitive machine learning method that uses support vector regression to identify active TREs from GRO-seq data without requiring cap-based enrichment. dREG allows TREs to be assayed together with…

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