Introduction to the Genboree Workbench

Genboree Workbench Home Page

Video Tutorial - Introduction to the Genboree Workbench

FAQs Related to Genboree Workbench Basics

Bioinformatics Tools for Analysis of Extracellular RNAs (exRNAs) in the Genboree Workbench

Small RNA-Seq Data Analysis for exRNA Profiling Using exceRpt Small RNA-seq Pipeline


Understanding exceRpt Results

Tool Version Updates

Long RNA-Seq Data Analysis Using RSEQtools

View Screencast (no audio)


Detecting Circular and Linear Isoforms from RNA-seq Data Using KNIFE


Performing Differential Expression Analysis (Fold Change Calculation) Using DESeq2


Performing Pathway and Interaction Analysis Using the Genboree Workbench

Target Interaction Finder

This tool generates miRNA-protein target interaction files for a set of miRNA identifiers,
which can be imported into downstream tools, such as Cytoscape, for network analysis and visualization.

View Screencast below (no audio):


Pathway Finder

This tool performs a search for pathways either containing miRNAs of interest
or protein targets of those miRNAs.

View Screencast below (no audio):


Demos at ExRNA Communication Consortium (ERCC) Meetings

  • May 2014 - Demo of small and long RNA-Seq pipelines at the ERCC 2nd Investigators' Meeting, May 2014, at Bethesda, MD
  • November 2014 - Demo of small RNA-seq pipeline and use cases presented at the ERCC 3rd Investigators' Meeting, November 2014, at Rockville, MD
  • April 2015 - Demo of small RNA-seq pipeline and use cases presented at the ERCC 4th Investigators' Meeting and ISEV Annual Meeting, April 2015, at Bethesda, MD
  • May 2015 - CIBR RNA-seq workshop - Demo of exceRpt small RNA processing pipeline, May 2015, at Baylor College of Medicine, Houston, TX
  • November 2015 - Data Submission & Analysis Infrastructure at the DMRR - Talk at the ERCC 5th Investigators' Meeting, November 2015, at Rockville, MD
  • April 2016 - DMRR Data Analysis and Bioinformatics Workshop at the ERCC 6th Investigators' Meeting, April 2016, at Bethesda, MD
  • May 2016 - Poster presentation on exRNA Atlas and exRNA Virtual Biorepository at the ISEV 2016 Annual Meeting, May 2016, at Rotterdam, The Netherlands

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