> ## Documentation Index
> Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt
> Use this file to discover all available pages before exploring further.
# 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
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.
Please note that for H5AD files greater than 10GB, it may take up to 5-10
minutes to launch the Pod.{" "}
When a Pod is launched for the first time, the following steps occur:
1. A computer instance is started with the default configuration of 8 CPUs and 32 GiB RAM.
2. The necessary file is downloaded from Latch Data into the Pod.
3. The `cellxgene launch` command 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.
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.
First, navigate to the [Latch Pods](https://console.latch.bio/apps) tab. It should be fourth tab on the left navigation sidebar. You should see the CELLxGENE pod that you just opened.
Click on **Manage Pod**.
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.
Don't worry, all the dependencies and files are fully preserved inside the Pod during the scaling process.
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
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.
Please follow the instructions [here](/pods/ssh#set-up-ssh-access) 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.
```bash theme={null}
nano /opt/latch/custom_app
```
Please follow the instructions [here](/pods/ssh#set-up-ssh-access) to SSH into your Pod.
To see the logs, type the following command:
```bash theme={null}
journalctl -f -b --user-unit latch-custom-app
```
## 2: Start a new CELLxGENE Pod session
### Frequently Asked Questions