RGD Tool and Website Tutorials

JBrowse Genome Browser       

This video will demonstrate how to use the RGD JBrowse Genome Browser. The JBrowse Genome Browser allows the user to view objects such as genes, variants, QTLs, and so forth in their genomic context. You can view versions for Rat, Human and Mouse.

Molecular Pathway Diagrams

This video will demonstrate how to use the RGD Molecular Pathway Diagrams. You can access the Ontology Report for the pathway, view the description for the pathway with it's various interactions and components, and you can click on any of the pathway's interactive features to view more information about that entity.

OLGA-Object List Generator and Analyzer

The purpose of OLGA is to build lists for rat genes, QTLs and strains. OLGA can also be used to query human and mouse genes and QTLs. Search for genomic data annotated to specific diseases, conditions and other queries. Multiple searches will allow you to refine your final result list to use for your own analysis or to send to another tool on the RGD website.

Variant Visualizer

The examination of SNPs has undergone a recent change, and in response to this change, RGD has released the new Variant Visualizer tool (VarVis), taking the place of the old SNPlotyper tool. VarVis is a visualization and analysis tool for sequence variation. The data currently contains 22 rat strains sequenced by 4 independent labs.

Gene Annotator Tool

The Gene Annotator takes a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, and/or a chromosomal region, and retrieves annotation data from RGD. This tool will retrieve annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases.

Gene Report Pages Tutorial

RGD’s new gene report pages are an even faster way of learning valuable information on genes, QTLs, markers, and strains. This informative video will show you each area of the report page, as well as how to view a gene and its annotations.

Physiological Pathway Diagrams Tutorial

Are you looking for a more intuitive way to visualize system-level pathway information? RGD's video tutorial about the Physiological Pathway diagrams will help you navigate these interactive diagrams for use as either a research or study tool.

Introduction to the RGD Phenotypes and Models Portal

In addition to genomic and genetic data, RGD is an excellent source of information about rat strains and their associated physiology, phenotypes and diseases.  This video will demonstrate how to navigate through the sections of RGD's Phenotypes and Models portal, so you can easily access the information you need.  Click the icon to get started.
SNPlotyper Tutorial Video

Finding Polymorphic Rat SNPs Using RGD's SNPlotyper Tool

Click this icon to access a short video tutorial demonstrating how to use the prototype of RGD's updated SNPlotyper tool to identify polymorphic markers between rat strains.


When it Comes to the Rat Genome, Bigger is Better

RGD's GViewer is an interactive tool which allows users to view genomic features such as genes and QTLs in the context of the entire genome.  Click this icon to access a short video tutorial on how to get started with the GViewer.

 Pathway diagram with arrow

It's Easy to Get Lost on the Biological Superhighway.  Thankfully, we Brought a Map.

Biological pathways are complex networks made up of a wide variety of components interacting in many different ways.  Click this icon to access a short video tutorial which demonstrates how RGD’s Interactive Pathway Diagrams can help you explore and understand these important intermolecular networks.

 Cancer Portal with arrow

Some Prefer Blue Jeans...RGD Prefers Disease Genes

RGD's Disease Portals consolidate data for each of a variety of disease areas, including Neurological Diseases, Cardivascular Diseases, Obesity/Metabolic Syndrome and Urogenital/Breast Cancer, into one integrated unit.  Click this icon to view a brief video detailing how you can use these portals to explore data related to these important areas of research.