Welcome! This Galaxy instance is being developed and maintained by members of the Hide Lab at the Harvard School of Public Health in association with the Harvard Stem Cell Institute.

Screencast Tutorial

Watch this video. You'll be glad you did!

A quick start to using SCDE Tools in Galaxy

You can access additional Galaxy screencasts at the main Galaxy site.

Customized Features



How to use Galaxy

To your left is the TOOLS panel. Use this to select one of the SCDE tools.
To your right is the HISTORY panel. Use this to track your uploaded files and your analysis results
Access the Help menu at the top of the page

Expand the Tools lists by clicking the linked headings

You can view and manipulate items in your History:
Display the data in your browser
Edit the attributes of the history item, e.g. its name
Delete the item from your History

Clicking on the History item name provides a preview of the data and some additional functions:
Download data
View details for this data
Run this job again

By clicking the icon to run a job again, you can also view the parameter values that were entered.

Get started with sample data

Two sample datasets that were generated by the Armstrong Lab are provided as examples.
  1. ARMSTRONG 16862118-Figure2bSRAS-standardized.txt: Genes displaying increased expression in HSC, L-GMP populations vs. CMP, MEP, GMP [Self-renewal associated signature (SRAS)]
  2. ARMSTRONG 20339075-Figure1b-standardized.txt: Increased expression in the HSC population (KLS cells) and L-GMP

Import datasets individually

To import each dataset into your History, click the link to the dataset. Then select the destination history or enter a name for a new history, and then click 'Import library datasets'.

Import datasets in batch from a saved history

Alternatively, hover your mouse over the 'Shared Data' link in the menu above, select 'Published Histories' and then click 'Example data'. You can then import the data into your History using the import history link.

Import datasets from the Data Library

Curated gene lists from the SCDE can also be accessed in this way, i.e. 'Shared Data' -> 'Data Libraries' -> 'SCDE Curated Gene Lists'

Once you have imported the data, you are ready to go ahead and use the tools.


The code for this Galaxy instance is available for download at the galaxy-central-hbc bitbucket repository.

The SCDE tool is available at the scde bitbucket repository.