Overview
- Introduction to the Genboree Workbench
- Bioinformatics Tools for Analysis of exRNA Atlas Data
- Running Analyses and Viewing Analysis Results Using the exRNA Atlas
- Bioinformatics Tools for Analysis of Your Own exRNA Data in the Genboree Workbench
- Small RNA-Seq Data Analysis for exRNA Profiling Using exceRpt Small RNA-seq Pipeline
- Long RNA-Seq Data Analysis Using RSEQtools
- 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
- Pathway Finder
- Demos at ExRNA Communication Consortium (ERCC) Meetings
Introduction to the Genboree Workbench¶
Video Tutorial - Introduction to the Genboree Workbench
FAQs Related to Genboree Workbench Basics
Bioinformatics Tools for Analysis of exRNA Atlas Data¶
Running Analyses and Viewing Analysis Results Using the exRNA Atlas¶
Bioinformatics Tools for Analysis of Your Own exRNA Data in the Genboree Workbench¶
Small RNA-Seq Data Analysis for exRNA Profiling Using exceRpt Small RNA-seq Pipeline¶
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