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Uploading Datasets to Omics Studio ​

This guide explains how to upload new datasets into Omics Studio. Each dataset is a collection of files (expression-matrices, statistics, sample metadata, and feature metadata) that can be used in studies and analyses. Once a dataset is created, its files cannot be changed, so ensure your files are complete and correctly formatted before uploading.

1. Access the Datasets page ​

  1. From the Workspace sidebar, click Datasets. The page lists all existing datasets and shows the number of datasets used.
  2. To create a new dataset, click the plus (+) button in the Dataset header row. A Create Dataset dialog opens.

2. Name your dataset ​

  1. In the Dataset Name field, type a descriptive name. Choose something meaningful, such as the experiment date or project name.
  2. Dataset names help organise multiple datasets and are displayed in the Datasets table.

3. Upload files ​

  1. Under the drop area, drag and drop your CSV files or click inside the dashed box to open a file-picker and select files from your computer.
  2. You can upload multiple files per dataset as long as the total size does not exceed 150 MB. Each file must be in CSV format.
  3. Common file types include:
    • Expression matrix – A table of expression or abundance values with features (e.g., genes, proteins) as rows and samples as columns.
    • Statistics file(s) – One or more CSV files containing statistical results such as fold changes and p-values. Each file should contain features in rows and statistical metrics in columns.
    • Feature metadata – A CSV file describing each feature (e.g., gene name, protein description, metabolite identifiers). This helps map identifiers to human-readable names.
    • Sample metadata – A CSV file describing your samples (e.g., sample ID, group assignments, clinical variables). This file becomes optional or mandatory depending on your analysis.
  4. As files are added, a progress bar shows the total upload size and a New Files list appears below the drop area. Check that all files appear correctly.

4. Finalise the dataset ​

  1. Review the New Files list to ensure all required files have been selected.
  2. Click Upload to create the dataset. Depending on file sizes, the upload may take a few minutes.
  3. Once the upload completes, the dialog closes and your dataset appears in the Datasets list. You can expand the dataset row to view its files and metadata.

Note: Uploaded files cannot be modified or deleted from a dataset. If you need to correct a file, create a new dataset with the corrected files.

Tips for preparing files ​

  • Consistent identifiers: Ensure that feature identifiers used across expression, statistics, and metadata files match (e.g., using the same gene or protein IDs).
  • CSV formatting: Use comma-separated values (CSV) and avoid Excel-specific formats. Quoted fields are allowed.
  • File sizes: Keep each individual file under 150 MB and ensure the total size across files does not exceed the platform limit.
  • File naming: Use clear file names (e.g., ExpressionMatrix.csv, Statistics1.csv, FeatureMetadata.csv) so they are easy to recognise when selecting files in Omics Studio.

By following these instructions you can upload your own data to Omics Studio and prepare it for downstream analyses. Once a dataset is uploaded, you can create studies using those files and perform various enrichment analyses.