CELLxGENE
CELLxGENE Explorer allows scientists to execute interactive analyses on a dataset to explore how patterns of gene expression are determined by environmental and genetic factors using an interactive speed no-code UI.
1: Select the H5AD file you want to visualize
First, navigate to the H5AD file that you want to visualize. If this is your first time on Latch, you will find an example H5AD file under the folder welcome/scbrowser/scanpy-pbmc3k.h5ad
2: Start a new CELLxGENE Pod session
When you open CELLxGENE on the file for the first time, a new Latch Pod will be created.
Latch Pod is a cloud-based computer that can scale up to 96 CPUs and 2TB of RAM, making it ideal for hosting interactive visualizations such as CELLxGENE, RShiny, Dash App, Jupyter Notebook, or RStudio.
For compute-intensive visualization of large single-cell datasets with over 1 million cells, the customizable Latch Pod is powerful, as you can increase the RAM as needed to accommodate growing datasets.
Once you click 'Create', you will see a status that indicates a Latch Pod is Launching.
Please note that for H5AD files greater than 10GB, it may take up to 5-10 minutes to launch the Pod.
FAQ: What contributes to the wait time?
FAQ: What contributes to the wait time?
When a Pod is launched for the first time, the following steps occur:
- A computer instance is started with the default configuration of 8 CPUs and 32 GiB RAM.
- The necessary file is downloaded from Latch Data into the Pod.
- The
cellxgene launchcommand is automatically executed on the downloaded file.
All these steps together can incur a few minutes of wait time, depending on the input data size.
Start Visualizing!
The CellXGene pod will open automatically.
(Optional) 3: Change the compute resources for CELLxGENE
Sometimes, it’s often desirable for single-cell applications to increase the computer’s RAM for compute-intensive steps, such as computing TSNE and PCA, or running differential expression analyses.
Because CELLxGENE is directly hosted on a Latch Pod that you have direct access to, changing the underlying resource profile is easy.
Navigate to Latch Pods
First, navigate to the Latch Pods tab. It should be fourth tab on the left navigation sidebar. You should see the CELLxGENE pod that you just opened.
Open the Pod Manager
Click on Manage Pod.
Modify Compute
Scroll down to the Compute & Storage section, modify the cores and RAM, and click Update.
It will take a few seconds for your Pod to scale up.
View the Updatted Resources
Once the Pod finishes scaling up, you can verify the new resource profile on the sidebar.
(Optional) 4: Turn off the Pod to save costs
Once you finish your analysis, you can go to the Pod and click the Stop button to shut down the Pod.
Frequently Asked Questions
Can I open multiple h5ad files per Pod?
Can I open multiple h5ad files per Pod?
Currently, only one h5ad file can be visualized in a single Pod at a time. To visualize a different h5ad file, you must manually stop the Pod, restart it, and then select the new h5ad file.
This restriction is in place because CELLxGENE opens a new session for each file. This approach ensures that your session remains undisturbed by other users who might want to visualize their files.
(Advanced) I'm a developer and want to modify the startup script in my Pod when an h5ad file is selected. How do I do that?
(Advanced) I'm a developer and want to modify the startup script in my Pod when an h5ad file is selected. How do I do that?
Please follow the instructions here to SSH into your Pod.
The startup script is located at /opt/latch/custom_app. You can use a code editor like vim or nano to modify the script.
(Advanced) My Pod is taking unusually long to start (10+ minutes). How can I see the logs to understand what may be wrong?
(Advanced) My Pod is taking unusually long to start (10+ minutes). How can I see the logs to understand what may be wrong?
Please follow the instructions here to SSH into your Pod.
To see the logs, type the following command:
CELLxGENE
CELLxGENE Explorer allows scientists to execute interactive analyses on a dataset to explore how patterns of gene expression are determined by environmental and genetic factors using an interactive speed no-code UI.
1: Select the H5AD file you want to visualize
First, navigate to the H5AD file that you want to visualize. If this is your first time on Latch, you will find an example H5AD file under the folder welcome/scbrowser/scanpy-pbmc3k.h5ad
2: Start a new CELLxGENE Pod session
When you open CELLxGENE on the file for the first time, a new Latch Pod will be created.
Latch Pod is a cloud-based computer that can scale up to 96 CPUs and 2TB of RAM, making it ideal for hosting interactive visualizations such as CELLxGENE, RShiny, Dash App, Jupyter Notebook, or RStudio.
For compute-intensive visualization of large single-cell datasets with over 1 million cells, the customizable Latch Pod is powerful, as you can increase the RAM as needed to accommodate growing datasets.
Once you click 'Create', you will see a status that indicates a Latch Pod is Launching.
Please note that for H5AD files greater than 10GB, it may take up to 5-10 minutes to launch the Pod.
FAQ: What contributes to the wait time?
FAQ: What contributes to the wait time?
When a Pod is launched for the first time, the following steps occur:
- A computer instance is started with the default configuration of 8 CPUs and 32 GiB RAM.
- The necessary file is downloaded from Latch Data into the Pod.
- The
cellxgene launchcommand is automatically executed on the downloaded file.
All these steps together can incur a few minutes of wait time, depending on the input data size.
Start Visualizing!
The CellXGene pod will open automatically.
(Optional) 3: Change the compute resources for CELLxGENE
Sometimes, it’s often desirable for single-cell applications to increase the computer’s RAM for compute-intensive steps, such as computing TSNE and PCA, or running differential expression analyses.
Because CELLxGENE is directly hosted on a Latch Pod that you have direct access to, changing the underlying resource profile is easy.
Navigate to Latch Pods
First, navigate to the Latch Pods tab. It should be fourth tab on the left navigation sidebar. You should see the CELLxGENE pod that you just opened.
Open the Pod Manager
Click on Manage Pod.
Modify Compute
Scroll down to the Compute & Storage section, modify the cores and RAM, and click Update.
It will take a few seconds for your Pod to scale up.
View the Updatted Resources
Once the Pod finishes scaling up, you can verify the new resource profile on the sidebar.
(Optional) 4: Turn off the Pod to save costs
Once you finish your analysis, you can go to the Pod and click the Stop button to shut down the Pod.
Frequently Asked Questions
Can I open multiple h5ad files per Pod?
Can I open multiple h5ad files per Pod?
Currently, only one h5ad file can be visualized in a single Pod at a time. To visualize a different h5ad file, you must manually stop the Pod, restart it, and then select the new h5ad file.
This restriction is in place because CELLxGENE opens a new session for each file. This approach ensures that your session remains undisturbed by other users who might want to visualize their files.
(Advanced) I'm a developer and want to modify the startup script in my Pod when an h5ad file is selected. How do I do that?
(Advanced) I'm a developer and want to modify the startup script in my Pod when an h5ad file is selected. How do I do that?
Please follow the instructions here to SSH into your Pod.
The startup script is located at /opt/latch/custom_app. You can use a code editor like vim or nano to modify the script.
(Advanced) My Pod is taking unusually long to start (10+ minutes). How can I see the logs to understand what may be wrong?
(Advanced) My Pod is taking unusually long to start (10+ minutes). How can I see the logs to understand what may be wrong?
Please follow the instructions here to SSH into your Pod.
To see the logs, type the following command: