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Supported Data Formats

!!! info "About this guide" This guide provides a basic overview of file formats and data supported in the ODM. For a detailed description and instructions on using various data formats and working with them (sorting, filtering, sampling), visit the Supported Data Formats page in our Advanced User Guide.

  • :octicons-table-16: TSV (Tabular data)

    Upload and manage tabular data (TSV files) seamlessly within the ODM. Work with Samples, Libraries, Preparations, Expression data, and more.

  • :fontawesome-solid-signal:{ .lg .middle } GCT (Gene Expression)

    Upload and work with GCT (Gene Cluster Text) files in the Open Data Manager (ODM). Optimize the analysis of matrix-compatible datasets.

  • :material-dna:{ .lg .middle } VCF (Variants)

    Upload and work with VCF (Variant Call Format) files to search, filter, retrieve, and analyze genetic variants in the ODM.

  • :fontawesome-solid-disease:{ .lg .middle } HDF5 (e.g. Single Cell)

    Upload and store HDF5 (Hierarchical Data Format 5) files as attachments in the ODM. Future releases will enable seamless analysis of Single Cell data stored within TSV and HDF5 formats.

  • :fontawesome-solid-wave-square:{ .lg .middle } FACS (Flow Cytometry)

    Upload and work with FACS (Fluorescence-Activated Cell Sorting) files in the Open Data Manager (ODM) to efficiently analyze Flow Cytometry data.

  • :fontawesome-solid-file-lines:{ .lg .middle } Attached Files

    Upload and organize a diverse range of attached non-indexed files in the ODM. Easily manage your entire data catalog, access and collaboration across any file types.

TSV (Tabular data)

In ODM, you can upload any tabular data formatted as TSV (tab-separated values). As long as your file represents a data frame, ODM can import and index it. A data frame is a data structure that organizes data into a two-dimensional table of rows and columns, similar to a spreadsheet.

A data frame contains two main elements:

  • Features: These are the entities measured in an experiment (e.g., genes, proteins, metabolites, pathways, sales regions, etc.).
  • Measurements (or values): These are the actual values recorded for each feature under different conditions (e.g., gene expression values, protein abundance, pathway activity, sales volume, etc.).

Simple Data Frame

The example below demonstrates the simplest and most common type of data frame.

Data Frame Simple

Here, the features (genes) are listed in the first column, while the rest of the table contains measurements of gene expression across multiple samples. Each column represents a different sample, with the column name indicating the corresponding dataset of gene expression values.

Complex Data Frame

Data Frame Complex

This format provides a wide range of data types that can be uploaded and indexed in ODM.

For a detailed description and instructions on using TSV, visit the Supported Data Formats page in our Advanced User Guide.

GCT (Gene xpression)

For a detailed description and instructions on using GCT, visit the Supported Data Formats page in our Advanced User Guide.

VCF (Variants)

For a detailed description and instructions on using VCF, visit the Supported Data Formats page in our Advanced User Guide.

HDF5 (e.g. Single Cell)

For a detailed description and instructions on using HDF5, visit the Supported Data Formats page in our Advanced User Guide.

FACS (Flow Cytometry)

For a detailed description and instructions on using FACS, visit the Supported Data Formats page in our Advanced User Guide.

Attached Files

For a detailed description and instructions on using Attached Files, visit the Supported Data Formats page in our Advanced User Guide.