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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…
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HOMER
Desktop

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…

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dREG
Desktop

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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MirSTP
Desktop

MirSTP MIRna transcription Start sites Tracking Program

Identifies active microRNA transcription start sites (miRNA TSSs) from nascent…

Identifies active microRNA transcription start sites (miRNA TSSs) from nascent transcriptomes. MirSTP provides accurate TSS prediction for human intergenic miRNAs at a high resolution by using…

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groHMM
Desktop

groHMM

Defines the boundaries of transcription units de novo using a two state…

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 transcriptional…

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CIPHER
Desktop

CIPHER

Automates the processing and analysis of several commonly used Next Generation…

Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease…

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Vespucci
Desktop

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…

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FStitch
Desktop

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…

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