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rewrite SUMMARY (doc reorg) (#4149)
Co-authored-by: Dr. Ernie Prabhakar <[email protected]> Co-authored-by: QuiltSimon <[email protected]>
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docs/README.md

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<!-- markdownlint-disable -->
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[![docs on_gitbook](https://img.shields.io/badge/docs-on_gitbook-blue.svg?style=flat-square)](https://docs.quiltdata.com/)
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[![chat on_slack](https://img.shields.io/badge/chat-on_slack-blue.svg?style=flat-square)](https://slack.quiltdata.com/)
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# Quilt is a data mesh for connecting people with actionable data
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## Python Quick start, tutorials
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If you have Python and an S3 bucket, you're ready to create versioned datasets with Quilt.
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Visit the [Quilt docs](https://docs.quiltdata.com/installation) for installation instructions,
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a quick start, and more.
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## Quilt in action
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* [open.quiltdata.com](https://open.quiltdata.com/) is a petabyte-scale open
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data portal that runs on Quilt
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* [quiltdata.com](https://quiltdata.com) includes case studies, use cases, videos,
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and instructions on how to run a private Quilt instance
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* [Versioning data and models for rapid experimentation in machine learning](https://medium.com/pytorch/how-to-iterate-faster-in-machine-learning-by-versioning-data-and-models-featuring-detectron2-4fd2f9338df5)
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shows how to use Quilt for real world projects
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## Who is Quilt for?
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Quilt is for data-driven teams and offers features for coders (data scientists,
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data engineers, developers) and business users alike.
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## What does Quilt do?
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Quilt manages data like code so that teams in machine learning, biotech,
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and analytics can experiment faster, build smarter models, and recover from errors.
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## How does Quilt work?
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Quilt consists of a Python client, web catalog, lambda
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functions&mdash;all of which are open source&mdash;plus
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a suite of backend services and Docker containers
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orchestrated by CloudFormation.
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The backend services are available under a paid license
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on [quiltdata.com](https://quiltdata.com).
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## Use cases
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* **Share** data at scale. Quilt wraps AWS S3 to add simple URLs, web preview for large files, and sharing via email address (no need to create an IAM role).
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* **Understand** data better through inline documentation (Jupyter notebooks, markdown) and visualizations (Vega, Vega Lite)
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* **Discover** related data by indexing objects in ElasticSearch
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* **Model** data by providing a home for large data and models that don't fit in git, and by providing immutable versions for objects and data sets (a.k.a. "Quilt Packages")
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* **Decide** by broadening data access within the organization and supporting the documentation of decision processes through audit-able versioning and inline documentation
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# Quilt: A Data Lakehouse for Actionable Data
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Quilt connects teams to actionable data by simplifying data discovery, sharing,
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and analysis. It’s designed to serve data-driven organizations with powerful
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tools for managing data as code, enabling rapid experimentation, and ensuring
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data integrity at scale.
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---
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## Navigating the Documentation
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The Quilt documentation is structured to guide users through different layers of
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the platform, from basic concepts to advanced integrations. Whether you're a
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business user, developer, or platform administrator, the docs will help you
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quickly find the information you need.
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### Quilt Platform Overview
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The **Quilt Platform** powers the core features of the Quilt data catalog,
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providing tools for browsing, searching, and visualizing data stored in AWS S3.
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The platform is ideal for teams needing to collaborate on data, with
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capabilities like embeddable previews and metadata collection.
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**Core Sections:**
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- [Architecture](Architecture.md) - Learn how Quilt is architected.
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- [Mental Model](MentalModel.md) - Understand the guiding principles behind
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Quilt.
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- [Metadata Management](Catalog/Metadata.md) - Manage metadata at scale.
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For users of the Quilt Platform (often referred to as the Catalog):
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- [Bucket Browsing](Catalog/FileBrowser.md) - Navigate through S3 buckets.
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- [Document Previews](Catalog/Preview.md) - Visualize documents and datasets
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directly in the web interface.
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- [Search & Query](Catalog/SearchQuery.md) - Leverage Quilt’s powerful search
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and querying capabilities.
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- [Visualization & Dashboards](Catalog/VisualizationDashboards.md) - Create
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visual dashboards for data insights.
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For administrators managing Quilt deployments:
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- [Admin Settings UI](Catalog/Admin.md) - Control platform settings and user
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access.
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- [Catalog Configuration](Catalog/Preferences.md) - Set platform preferences.
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- [Cross-Account Access](CrossAccount.md) - Manage multi-account access to S3
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data.
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### Quilt Python SDK
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The **Quilt Python SDK** allows users to programmatically manage data packages,
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version datasets, and automate data workflows. Whether you're uploading a
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package, fetching data, or scripting custom workflows, the SDK provides the
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flexibility needed for deeper integrations.
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- [Installation](Installation.md) - Get started with the Quilt SDK.
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- [Quick Start](Quickstart.md) - Follow a step-by-step guide to building and
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managing data packages.
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- [Editing and Uploading Packages](walkthrough/editing-a-package.md) - Learn how
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to version, edit, and share data.
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- [API Reference](api-reference/api.md) - Detailed API documentation for
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developers.
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### Quilt Ecosystem and Integrations
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The **Quilt Ecosystem** extends the platform with integrations and plugins to
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fit your workflow. Whether you're managing scientific data or automating
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packaging tasks, Quilt can be tailored to your needs with these tools:
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- [Benchling
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Packager](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
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- Package biological data from Benchling.
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- [Nextflow Plugin](examples/nextflow.md) - Integrate with Nextflow pipelines
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for bioinformatics.
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---
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## Who Should Use Quilt?
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Quilt is for teams across industries like machine learning, biotech, and
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analytics who need to manage large datasets, collaborate seamlessly, and track
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the lifecycle of their data. Whether you're a data scientist, engineer, or
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administrator, Quilt helps streamline your data management workflows.
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## What Can You Do with Quilt?
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- **Share**: Easily share versioned data using simple URLs and email invites.
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- **Understand**: Enrich data with inline documentation and visualizations for
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better insights.
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- **Discover**: Use metadata and search tools to explore data relationships
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across projects.
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- **Model**: Version and manage large data sets that don't fit traditional git
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repositories.
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- **Decide**: Empower your team with auditable data for better decision-making.
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---
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## How to Get Started
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To dive deeper into the capabilities of Quilt, start with our [Quick Start
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Guide](Quickstart.md) or explore the [Installation
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Instructions](Installation.md) for setting up your environment.
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If you have any questions or need help, join our [Slack
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community](https://slack.quiltdata.com/) or visit our full [documentation
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site](https://docs.quiltdata.com/).

docs/SUMMARY.md

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<!-- markdownlint-disable -->
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# Summary
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# Quilt Documentation
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* [Introduction](README.md)
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* [Installation](Installation.md)
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* [Quick start](Quickstart.md)
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* [Mental model](MentalModel.md)
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* [About Quilt](README.md)
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* [Architecture](Architecture.md)
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* [Mental Model](MentalModel.md)
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* [Metadata Management](Catalog/Metadata.md)
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* [Metadata Workflows](advanced-features/workflows.md)
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### Walkthrough
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* [Editing a Package](walkthrough/editing-a-package.md)
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* [Uploading a Package](walkthrough/uploading-a-package.md)
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* [Installing a Package](walkthrough/installing-a-package.md)
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* [Getting Data from a Package](walkthrough/getting-data-from-a-package.md)
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* [Working with the Catalog](walkthrough/working-with-the-catalog.md)
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* [Working with a Bucket](walkthrough/working-with-a-bucket.md)
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* [Working with Elasticsearch](walkthrough/working-with-elasticsearch.md)
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## Quilt Platform (Catalog) User
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* [About the Catalog](walkthrough/working-with-the-catalog.md)
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* [Bucket Browsing](Catalog/FileBrowser.md)
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* [Document Previews](Catalog/Preview.md)
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* [Embeddable iFrames](Catalog/Embed.md)
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* [Search & Query](Catalog/SearchQuery.md)
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* [Visualization & Dashboards](Catalog/VisualizationDashboards.md)
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* **Advanced**
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* [Athena](advanced-features/athena.md)
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* [Elasticsearch](walkthrough/working-with-elasticsearch.md)
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### API Reference
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* [quilt3](api-reference/api.md)
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* [quilt3.Package](api-reference/Package.md)
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* [quilt3.Bucket](api-reference/Bucket.md)
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* [quilt3.admin](api-reference/Admin.md)
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* [CLI, environment](api-reference/cli.md)
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* [Known limitations](api-reference/limitations.md)
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* [Custom SSL certificates](api-reference/custom-ssl-certificates.md)
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## Quilt Platform Administrator
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### Catalog
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* [Admin UI](Catalog/Admin.md)
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* [Configuration](Catalog/Preferences.md)
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* [Working with files](Catalog/FileBrowser.md)
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* [Embed](Catalog/Embed.md)
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* [Metadata for teams](Catalog/Metadata.md)
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* [Preview](Catalog/Preview.md)
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* [Search & query](Catalog/SearchQuery.md)
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* [Visualization & dashboards](Catalog/VisualizationDashboards.md)
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* [Local Development Mode](Catalog/LocalMode.md)
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* [Admin Settings UI](Catalog/Admin.md)
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* [Catalog Configuration](Catalog/Preferences.md)
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* [Cross-Account Access](CrossAccount.md)
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* [Enterprise Installs](technical-reference.md)
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* [quilt3.admin Python API](api-reference/Admin.md)
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* **Advanced**
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* [Package Events](advanced-features/package-events.md)
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* [Private Endpoints](advanced-features/private-endpoint-access.md)
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* [Restrict Access by Bucket Prefix](advanced-features/s3-prefix-permissions.md)
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* [S3 Events via EventBridge](EventBridge.md)
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* [SSO Permissions Mapping](advanced-features/sso-permissions.md)
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* **Best Practices**
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* [GxP for Security & Compliance](advanced-features/good-practice.md)
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* [Organizing S3 Buckets](advanced-features/s3-bucket-organization.md)
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### Examples
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* [Git-like operations for datasets and Jupyter notebooks](examples/GitLike.md)
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* [Nextflow](examples/nextflow.md)
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## Quilt Ecosystem Integrations
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### Advanced
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* [Filtering a Package](advanced-features/filtering-a-package.md)
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* [.quiltignore](advanced-features/.quiltignore.md)
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* [Materialization](advanced-features/materialization.md)
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* [Working with Manifests](advanced-features/working-with-manifests.md)
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* [S3 Select](advanced-features/s3-select.md)
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* [Workflows](advanced-features/workflows.md)
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* [Enterprise install](technical-reference.md)
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* [S3 Events, EventBridge](EventBridge.md)
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* [Cross-account access](CrossAccount.md)
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* [Restrict access to bucket prefixes](advanced-features/s3-prefix-permissions.md)
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* [Querying Metadata with Athena](advanced-features/athena.md)
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* [S3 Bucket Organization](advanced-features/s3-bucket-organization.md)
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* [Package events](advanced-features/package-events.md)
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* [Event-driven packaging](advanced-features/event-driven-packaging.md)
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* [GxP & Quilt](advanced-features/good-practice.md)
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* [Private endpoints](advanced-features/private-endpoint-access.md)
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* [SSO permissions mapping](advanced-features/sso-permissions.md)
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* [Benchling Packager](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
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* [Event-Driven Packaging](advanced-features/event-driven-packaging.md)
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* [Nextflow Plugin](examples/nextflow.md)
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### More
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* [Frequently Asked Questions](FAQ.md)
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* [Troubleshooting](Troubleshooting.md)
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* [Contributing](CONTRIBUTING.md)
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* [Changelog](CHANGELOG.md)
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## Quilt Python SDK Developers
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* [Installation](Installation.md)
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* [Quick Start](Quickstart.md)
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* [Editing a Package](walkthrough/editing-a-package.md)
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* [Uploading a Package](walkthrough/uploading-a-package.md)
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* [Installing a Package](walkthrough/installing-a-package.md)
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* [Getting Data from a Package](walkthrough/getting-data-from-a-package.md)
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* [Example: Git-like Operations](examples/GitLike.md)
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* **API Reference**
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* [quilt3](api-reference/api.md)
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* [quilt3.Package](api-reference/Package.md)
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* [quilt3.Bucket](api-reference/Bucket.md)
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* [Local Catalog](Catalog/LocalMode.md)
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* [CLI, Environment](api-reference/cli.md)
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* [Known Limitations](api-reference/limitations.md)
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* [Custom SSL Certificates](api-reference/custom-ssl-certificates.md)
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* **Advanced**
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* [Browsing Buckets](walkthrough/working-with-a-bucket.md)
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* [Filtering a Package](advanced-features/filtering-a-package.md)
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* [.quiltignore](advanced-features/.quiltignore.md)
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* [Manipulating Manifests](advanced-features/working-with-manifests.md)
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* [Materialization](advanced-features/materialization.md)
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* [S3 Select](advanced-features/s3-select.md)
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* **More**
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* [Changelog](CHANGELOG.md)
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* [Contributing](CONTRIBUTING.md)
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* [Frequently Asked Questions](FAQ.md)
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* [Troubleshooting](Troubleshooting.md)

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