This workspace uses JupyterLab in Terra on Azure to explore common Bioconductor packages that can be used to perform bulk RNA differential expression analyses or manipulate single-cell RNA-seq data.
Tutorial prerequisites
Step 1: Set up your workspace
1.1. Go to app.terra.bio.
1.2. Log in with your Microsoft account to use Terra on Azure.
1.3. From the welcome screen, navigate to Workspaces.
1.4. Select Bulk_and_Single-Cell_RNASeq_Analysis_with_Bioconductor from the Featured Workspaces list.
1.5. This Featured Workspace is read-only. To make your own copy of the workspace for completing the tutorial, go to the top right corner and select the circle with 3 dots. A drop down menu will appear and you will select clone.
1.6. Now you have your own copy of the workspace, you can get started.
Step 2: Start Jupyter notebooks
To run a Jupyter notebook analysis, you will need to set up the virtual machine that runs the Jupyter app. See How to customize and launch your JupyterLab.
2.1. From the Analyses tab in your workspace, click the Jupyter notebook titled “EdgeR.”
2.2. Once selected, you'll be prompted to start an Azure Cloud Environment.
VM configuration
- Under Cloud Compute profile, select the Standard_DS2_v2, 2 CPU(s), 7GBs profile.
What to expect
It may take 3-5 minutes to spin up. Once it's ready, you will see a green dot under the Jupyter logo in the right sidebar.
Step 3. Run the Notebook
Once the Azure Cloud environment creation is complete, you can open the notebook in JupyterLab. You also have the option to either pause or modify the Jupyter environment using ‘Settings’.
3.1. Click to Open JupyterLab with the .ipynb notebooks from the cloned workspace.
3.2. To start your analysis, open the edgeR.ipynb jupyter notebook from the left for editing.
3.3. Verify that the notebook is using the right kernel by checking the top right corner and bottom left corner of the browser page. It should be R.
To change the kernel for the current notebook, click on the left bottom kernel name. This could open a window with a dropdown list to select the kernel for the ‘edgeR.ipynb’ notebook
3.5. Run the analysis by following the instructions in the notebook.