Data Selection

The Data Selection tab is the initial step to upload and manage your data in cOmicsArt. This section is divided into two main areas: the side panel and the main panel.

Side Panel 📚

The side panel offers several tabs for different data input methods. The data Upload and possible structure are detailed in the Data Input. Nonetheless, here is a short overview:

File Input 🛠️

  • Omic Type that is uploaded: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics).

  • Upload data matrix: Upload your data matrix file. Rows should be entities (e.g., genes) and columns should be samples.

  • Upload sample annotation: Upload the sample annotation file. Rows should be samples.

  • Upload entities annotation matrix: Upload the entities annotation matrix file.

  • Inspect data: Click this button to inspect the uploaded data. This will open a Modal, in which you can see how the application interprets your data, whether it is able to differentiate between the different columns and - through additional tests - whether the data as you uploaded it is deemed good to go.

  • Upload new data: Click this button to upload new data files.

Precompiled 🔧

  • Omic Type that is uploaded: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics).

  • Load precompiled data: Upload a precompiled data file (e.g., RDS file). It has the benefit, that - once saved - you only need to upload a single file now instead of all three.

  • Upload new data: Click this button to upload new precompiled data files.

Metadata

Very similar to the File Input, but replacing the sample annotation with the Metadatasheet.

  • Omic Type that is uploaded: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics).

  • Upload data matrix: Upload your data matrix file. Rows should be entities (e.g., genes) and columns should be samples.

  • Upload your Meta Data Sheet: Upload your metadata sheet. This currently replaces the sample annotation.

  • Upload entities annotation matrix: Upload the entities annotation matrix file. Rows should be entities.

  • Upload new data: Click this button to upload new metadata files.

Testdata 🧪

  • Omic Type that is uploaded: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics).

  • Upload data: Click this button to start with a test dataset.

Main Panel 💡

The main panel provides options for detailed data selection:

  • (Optional) Adding Gene Annotation: In case of transcriptomics data, you can add gene annotation to your sample. For this you only need to choose Which Organism? ** and click the **Add Gene Annotation button. This will add the entrez gene ids, ensemble gene ids, gene symbols and gene biotype (e.g. protein coding, etc.) to your data.

Row Selection - Biochemical Entities

  • Which annotation type do you want to select on?: Here you select a column of your entitie annotation. Based on this column you can then select specific rows to include through Which entities to use?. This might be either entitie names or depending on the column you select also functional groups like e.g. “All Protein Coding Genes”. The more information you have on your entities, the better you can select here.

Sample Selection

  • Which annotation type do you want to select on?: Similar to the row selection you select a column of your sample annotation. Based on this column you can then select specific samples to include through Which entities to use?. You can e.g. select specific samples or all samples from a specific experiment. Again, the more information you have on the samples, the better you can choose here.

Save Input As RDS 💾

  • Save file input to upload later: Click this button to save the file input as an RDS file for later use.

Start the Journey 🚀

  • Start the Journey: Click this button to proceed with the analysis. This will automatically bring you to the Pre-processing tab.

Other Notes 📌

  • Question Marks: The displayed question marks provide quick and immediate help. They offer guidance and additional information about the options available.

Further Navigation

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