Uploading data files

Studies in Single Cell Portal can serve as visualization portals, data repositories, or both. Certain files* are needed for visualization and, if supplied, will automatically be used to build a visualization portal for your study. If these files are not provided, others can still download your data you have provided. If visualization files and other data files are provided, other users will automatically be able to both visualize and download the data. When a study is created, it can be set as private or public, and this status also applies to any associated data. Visit here to learn more about permissions for studies and data.

*As of July 5th 2023 AnnData file upload has been released in Beta mode. This feature allows you to upload a single AnnData file in place of separate Expression files, Clustering files and a Metadata file.

Overview of the upload wizard

When creating a new study, you will be brought to an upload wizard to walk through data upload. Below is the first step of the upload wizard in which you will need to choose between the Classic and AnnData (BETA) experiences. The Classic experience will require multiple files for visualization while the AnnData experience requires a single AnnData file for visualization.

Choosing "Classic" will bring you to this view:

1. These tabs track which step you are on as you progress in the wizard. Once a file has been uploaded the number in the white circle will be replaced by a check mark to indicate that a step has been completed.
2. Description of the step and associated data for upload.
3. Example data, which you can download to help you format your own data.
4. Click "Choose File" to choose the file to upload.
5. For cluster/spatial files, choose a short name that describes the plot in the file. Otherwise, the loaded file's name will be used. (Name choice not available for most file types)
6. Enter a description of the file here.
7. "Save" and "Delete" can be used to save current progress, update text changes or delete files.
8. "Next" can be used to move to the next step without loading the current step file. Once all required files for visualization are loaded the portal will automatically create pages to visualize the study.
9. "Previous" allows access to the previous step in case files need to be reloaded.
10. "Switch to AnnData upload" allows you to switch to the AnnData upload mode. This button will be visible as long as you have not uploaded a file yet. Once you upload a file you will not be able to switch modes.
11. These indicators "No clustering visuals" and "No expression visuals" will update as you upload the appropriate files to create visualizations. Hovering over them will let you know which files are missing for visualizations.

Choosing AnnData mode from the initial page of the upload wizard will lead to the following view:

1. These tabs track which step you are on as you progress in the wizard. 
2. Description of the step or further instructions for that step.
3. Click "Choose File" to choose the file to upload. You will not have the option to upload a separate Expression matrix, Metadata or Clustering file; instead, you will upload the single AnnData file in place of these in the AnnData tab.
4. Enter a description of the file here.
5. "Save" and "Delete" can be used to save current progress, update text changes or delete files.
6. "Next" can be used to move to the next step without loading the current step’s file. Once all files that are required for visualization are loaded, the portal will automatically create pages to visualize the study.
7. "Previous" allows access to the previous step in case files need to be reloaded.
8. "Switch to Classic upload" allows you to switch to the Classic upload mode. This button will be visible as long as you have not uploaded a file yet. Once you upload a file you will not be able to switch modes.

In either mode (Classic or AnnData) as long as you have not uploaded any files you can toggle to the other mode using the "Switch to 'x' upload" button located near the top of the page. Once you upload a file the ability to switch between modes will go away.