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Thank you for testing our beta release of gEAR 2.0!

We are still working on the final version of the site. Please be aware that some features may not work as expected, though we've tried to put placeholders where we know things aren't yet finished. If you encounter any issues, please report them to us using the "Feedback" link in the user menu on the left.

Important!

This page is for testing and feedback. You are free to make changes, add data, perform analyses, etc. but changes will not be saved permanently while in beta mode.

Not logged in

You must be logged in to upload a dataset. Please log in (upper right) or create an account!.

Submissions in progress

This table has entries for any uploads you have in progress. Click to resume or see more details about the status.

Share ID Status Dataset type Title Actions

Or start a new submission:

  • Enter metadata

    Use the form or provided template to enter metadata for your dataset.

  • Upload dataset

    Choose your dataset format and upload directly or provide a supported URL.

  • Dataset processing

    Your dataset is processed and checked on the server.

  • Finalize submission

    Your dataset gets fully integrated into the system here.

  • Curate dataset

    Get the most out of your dataset by doing curation steps here.

Step - Enter metadata (via form OR upload)

The 'metadata' is the data describing your dataset, including things like title, authorship, sequencing protocols used, etc. This is the first step in uploading a dataset to the portal. All data uploaded are initially private to only your account (you can change this later in the Dataset Explorer)

Enter the metadata manually below OR fill out and upload from a spreadsheet template.

Annotation metadata

Contact, organism and instrumentation

Entry not found

If a GEO ID is available, enter it here and the rest can be autofilled.

Please check the form above and correct these issues.

    Step - Upload dataset

    Choose the format of your dataset and upload it here. You can also provide a URL to a supported dataset.

    MEX / 3-tab format

    These are simple, plain-text files in a bundle, usually compressed with tar/gzip or zip.

    Learn more

    • MEX info
    • MEX example
    • 3-tab info
    • 3-tab example

    MS Excel

    Similar in format to 3-tab but rather than individual files each is a different tab in an Excel spreadsheet. Mostly for bulk RNA-seq data as it doesn't initial-scale very well for even medium-sized datasets.

    Learn more

    • Excel info
    • Excel example

    Rdata / Seurat

    This is a binary format used by the Seurat package in R. If you've already been working with your dataset in R, including clustering and other analyses, this is the format to choose.

    Learn more

    • Rdata info
    • Rdata example

    H5AD / Python

    Usually created by the Scanpy package in Python, this is a binary format that is very efficient for large datasets. If you've been working with your dataset in Python, this is the format to choose.

    Learn more

    • H5AD info
    • H5AD example

    Step - Process dataset

    Your dataset is being processed on the server. This may take a few minutes, depending on the size of the dataset. You can close your browser at any time and return to the uploader to check on the progress.

    Status: Checking ...

    Message:

    Step - Finalize submission

    Your dataset has been processed and is ready to be submitted.

    Please use the Feedback link on the left and provide this error message:

    Steps being performed:

    • Storing metadata
    • Migrate H5AD file
    • Migrate user-uploaded source file
    • Setting access rights

    Step - Curate dataset

    Your dataset has been submitted and is now available in the Dataset Explorer.

    What is curation?

    Right now your dataset is stored in the system but there are no visualizations created so users can explore it. Curation is the process of creating these visualizations, which can include things like bar charts, UMAPs, heatmaps, etc.

    Dataset curation examples