# Panomics Documentation ## Panomics Documentation - [Overview](https://documentation.panomics.bio/documentation/readme.md) - [Projects](https://documentation.panomics.bio/documentation/projects.md): Learn to use projects to collaborate, organize your work, and control access to files. - [Project Structure](https://documentation.panomics.bio/documentation/projects/project-structure.md): Learn about the 5 sections of every Panomics project. - [Project Visibility](https://documentation.panomics.bio/documentation/projects/project-visibility.md) - [Project Access](https://documentation.panomics.bio/documentation/projects/project-access.md) - [Samples](https://documentation.panomics.bio/documentation/samples.md) - [Sample Lifecycle](https://documentation.panomics.bio/documentation/samples/sample-lifecycle.md) - [Sample Ingestion](https://documentation.panomics.bio/documentation/samples/sample-ingestion.md) - [Sample Metadata](https://documentation.panomics.bio/documentation/samples/sample-metadata.md) - [Analyses](https://documentation.panomics.bio/documentation/analyses.md): Learn how to analyze omics samples with zero lines of code - [Create an Analysis](https://documentation.panomics.bio/documentation/analyses/create-an-analysis.md) - [Delete an Analysis](https://documentation.panomics.bio/documentation/analyses/delete-an-analysis.md) - [Change Analysis Status](https://documentation.panomics.bio/documentation/analyses/change-analysis-status.md) - [Publish an Analysis](https://documentation.panomics.bio/documentation/analyses/publish-an-analysis.md) - [View Analysis Audit Trail](https://documentation.panomics.bio/documentation/analyses/view-analysis-audit-trail.md) - [Analysis Workbench](https://documentation.panomics.bio/documentation/analyses/analysis-workbench.md) - [Quality Control](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/quality-control.md) - [Gene Expression](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/gene-expression.md) - [Compute Statistics](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/compute-statistics.md) - [Sample/Cell Explorer](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/sample-cell-explorer.md) - [Normalization](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/sample-cell-explorer/normalization.md) - [UMAP](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/sample-cell-explorer/umap.md) - [Cell Composition](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/cell-composition.md) - [Marker Genes](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/marker-genes.md) - [Differential Gene Expression](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/differential-gene-expression.md) - [Differential Pathway Activity](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/differential-pathway-activity.md) - [WGCNA](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/wgcna.md) - [Gene Set Enrichment](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/gene-set-enrichment.md) - [Data Slices](https://documentation.panomics.bio/documentation/analyses/data-slices.md) - [OmicsBrowser](https://documentation.panomics.bio/documentation/omicsbrowser.md) - [Gene Signature Similarity](https://documentation.panomics.bio/documentation/gene-signature-similarity.md) - [Compute Runtimes](https://documentation.panomics.bio/documentation/compute-runtimes.md): Run bioinformatics computations in Panomics with on-demand runtimes. - [Codeless Compute](https://documentation.panomics.bio/documentation/compute-runtimes/codeless-compute.md): User friendly, point and click analyses. - [Code-based Compute](https://documentation.panomics.bio/documentation/compute-runtimes/code-based-compute.md): Spin-up JupyterLab or RStudio runtimes to run custom bioinformatics analyses. - [API Keys](https://documentation.panomics.bio/documentation/api-keys.md) - [Access Control](https://documentation.panomics.bio/documentation/access-control.md) - [Overview](https://documentation.panomics.bio/documentation/access-control/overview.md) - [What you can do with access control](https://documentation.panomics.bio/documentation/access-control/overview/capabilities.md) - [Quick start: Give a team access in 2 minutes](https://documentation.panomics.bio/documentation/access-control/overview/quick-start.md) - [Core Concepts](https://documentation.panomics.bio/documentation/access-control/concepts.md) - [Teams](https://documentation.panomics.bio/documentation/access-control/concepts/teams.md) - [Resources & hierarchy](https://documentation.panomics.bio/documentation/access-control/concepts/resources-hierarchy.md) - [Inheritance & overrides](https://documentation.panomics.bio/documentation/access-control/concepts/inheritance-overrides.md) - [Umbrella actions & admin](https://documentation.panomics.bio/documentation/access-control/concepts/umbrella-admin.md) - [Resource Access Window (UI guide)](https://documentation.panomics.bio/documentation/access-control/ui.md) - [Inherited permissions](https://documentation.panomics.bio/documentation/access-control/ui/inherited.md) - [Direct permissions](https://documentation.panomics.bio/documentation/access-control/ui/direct.md) - [Child resource permissions](https://documentation.panomics.bio/documentation/access-control/ui/children.md) - [System Teams](https://documentation.panomics.bio/documentation/access-control/system-teams.md) - [All Users](https://documentation.panomics.bio/documentation/access-control/system-teams/all-users.md) - [Guest](https://documentation.panomics.bio/documentation/access-control/system-teams/guest.md) - [How‑to / Common Recipes](https://documentation.panomics.bio/documentation/access-control/recipes.md) - [Internal public project](https://documentation.panomics.bio/documentation/access-control/recipes/internal-public-project.md) - [Project-wide analysis access](https://documentation.panomics.bio/documentation/access-control/recipes/project-wide-analysis.md) - [Restrict a single analysis](https://documentation.panomics.bio/documentation/access-control/recipes/restrict-single-analysis.md) - [Guests by domain](https://documentation.panomics.bio/documentation/access-control/recipes/guests-by-domain.md) - [Read-only external collaborator (single Analysis)](https://documentation.panomics.bio/documentation/access-control/recipes/external-readonly-analysis.md) - [Data manager for project assets](https://documentation.panomics.bio/documentation/access-control/recipes/data-manager-assets.md) - [Public Bio-App catalog](https://documentation.panomics.bio/documentation/access-control/recipes/public-bioapp-catalog.md) - [Permissions Reference](https://documentation.panomics.bio/documentation/access-control/reference.md) - [Generic actions](https://documentation.panomics.bio/documentation/access-control/reference/generic.md) - [Project actions](https://documentation.panomics.bio/documentation/access-control/reference/project.md) - [Analysis actions](https://documentation.panomics.bio/documentation/access-control/reference/analysis.md) - [Organization & User features](https://documentation.panomics.bio/documentation/access-control/reference/org-user.md) - [Glossary](https://documentation.panomics.bio/documentation/access-control/glossary.md) - [FAQ](https://documentation.panomics.bio/documentation/access-control/faq.md) - [Troubleshooting & gotchas](https://documentation.panomics.bio/documentation/access-control/troubleshooting.md) - [Administration](https://documentation.panomics.bio/documentation/administration.md) - [Users](https://documentation.panomics.bio/documentation/administration/users.md) - [Ontologies](https://documentation.panomics.bio/documentation/administration/ontologies.md) - [Metadata Fields](https://documentation.panomics.bio/documentation/administration/metadata-fields.md) - [Collections](https://documentation.panomics.bio/documentation/administration/collections.md) - [Gene Set Collections](https://documentation.panomics.bio/documentation/administration/gene-set-collections.md) - [Organization Settings](https://documentation.panomics.bio/documentation/administration/organization-settings.md) - [Release Notes](https://documentation.panomics.bio/documentation/release-notes.md) - [Technical Support](https://documentation.panomics.bio/documentation/technical-support.md): Contact the Panomics Support team for help in using the Platform. - [Legal](https://documentation.panomics.bio/documentation/legal.md) --- # Agent Instructions This documentation is published with GitBook. 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