Panomics Documentation
  • Overview
  • Projects
    • Project Structure
    • Project Visibility
    • Project Access
  • Samples
    • Sample Lifecycle
    • Sample Ingestion
    • Sample Metadata
  • Analyses
    • Create an Analysis
    • Delete an Analysis
    • Change Analysis Status
    • Publish an Analysis
    • View Analysis Audit Trail
    • Analysis Workbench
      • Quality Control
      • Gene Expression
      • Compute Statistics
      • Sample/Cell Explorer
        • Normalization
        • UMAP
      • Cell Composition
      • Marker Genes
      • Differential Gene Expression
      • Differential Pathway Activity
      • WGCNA
      • Gene Set Enrichment
    • Data Slices
  • OmicsBrowser
  • Gene Signature Similarity
  • Compute Runtimes
    • Codeless Compute
    • Code-based Compute
  • API Keys
  • Administration
    • Roles
    • Users
    • Ontologies
    • Metadata Fields
    • Collections
    • Gene Set Collections
    • Organization Settings
  • Release Notes
  • Technical Support
  • Legal
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  • Project Metadata
  • Analyses
  • Samples
  • Assets
  • Readme
  1. Projects

Project Structure

Learn about the 5 sections of every Panomics project.

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Last updated 1 month ago

All Panomics projects share a common structure that makes collaborative analysis straightforward.

Project Metadata

The project metadata can be split into 2 categories, each serving a specific purpose.

Direct Metadata

This helps team members understand what the project is all about. It includes:

  • title

  • external ID (e.g.: GEO identifier)

  • description

  • overall design

  • tags

Inherited Metadata

This is the metadata inherited from the samples associated with the project. It can include information about the tissue, disease, treatment compounds, etc. Projects can be filtered using any of the configured at the organization level.

Analyses

This is where all project analyses reside. From this section, users can:

  • list and filter all project analyses

  • mark analyses as done

  • publish or unpublish analyses

  • view audit trail

  • export analyses as cell atlases (applicable only to single cell analyses)

  • delete analyses

Samples

This is where all project samples reside.

Samples can be associated with more than one project.

From this section, users can:

  • list and filter all project samples

  • import new samples

  • remove samples from the project

  • upload/edit metadata

  • create new analyses

Assets

The Assets page functions as a versatile file explorer within Panomics. It allows users to manage project files by creating folders, uploading, downloading, and moving files.

For compute results, it offers a read-only view, with the option to copy analysis results to the JupyterLab or RStudio mounts.

The JupyterLab and RStudio mounts connect directly to the runtime’s shared drive, providing a secure way to transfer files to or from the project.

Readme

The readme is a collaborative document used to describe the analytical decisions made, write down hypothesis, or ask for feedback.

For more details, visit the .

change the samples' status (see )

For more details, visit the .

metadata fields
dedicated pages
sample lifecycle
dedicated pages
Analysis list
Sample list