Quick Start

Each page in Guide is self-cotained, and accessible from the menu items at the top of the page.

Each page performs some function, such as show a set of genes or expression profile for a gene in a dataset. Some pages will be launched automatically from other pages, such as the page of gene set after clicking on the search button from the differential expression page. All pages are accessible through the menus at any time.

Tutorial

Guide comes with an example dataset called "pickrell", which is a subset of the example dataset used in the "RNA-Seq Case Studies" chapter of limma user's guide, where the data originally comes from HapMap project (Pickrell, Joseph K., et al. Nature 464.7289 (2010): 768-772). This example dataset can be used to try out the various functionalities without having to upload data first.

To find a set of differentially expressed genes between males and females from this dataset, go to the differential expression analysis page, and select the dataset. You'll see a few available options once the dataset is selected. You can just leave all the available options as they are and click on the Search button. Guide should bring back a list of differentially expressed genes.

illustration of what each

The page that comes back is the gene sets page, which shows a list of differentially expressed genes. You can export the gene set table to a file by selecting "export gene set" button. This will show a tab-delimted text with all the columns shown in the table.

Gene set page

This is the page which shows a list of genes, whether as a result of doing a search for genes or perfroming differential expression analysis. This page has a number of useful features:

1. You can sort any of the columns by clicking on the column header. For example, to see the gene with the highest log fold change, click on the column header for "logFC" column.

2. You can view the expression profile of a particular gene by clicking on the dataset name in the Expression column.

3. Clicking on the feature link in the table will open up your browser to show details for the gene at NCBI website.

4. You can export the current gene set to tab-delimited file, using the "export gene set" options.

 

Creating custom R scripts

Wherever the "Show R Commands" button is available, editing the R scripts used by Guide can be modified. For example, if you wish to use an alternative method for finding differentially expressed genes, to the default method of limma and voom, you do so. The changes made will persist across sessions once saved.