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Foundry Connect Documentation
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Get Started
First Steps
First Steps
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Select Run Environment
Add Data
Run a Pipeline
Review Results
Wrap Up
Get to Know Pipelines
Get to Know Pipelines
What are Pipelines?
RNA Seq Pipeline
ATAC-Seq and ChIP-Seq pipelines
Why Foundry Connect?
Why Foundry Connect?
Benefits of Foundry Connect
Nextflow, Amplified
Public Pipelines
User Guides
User Guides
Profile Guide
Profile Guide
What is a Profile?
SSH Credentials
AWS Credentials
AWS Run Authentication Modes
Google Cloud Credentials
Integration Tokens
User Groups
Configure Run Environment
Data Guide
Data Guide
What are Datasets?
Creating Datasets
Upload Local Data
Upload Local Data
Using AWSCLI
Using GCP
Using Cyber Ducker
Cloud Solutions
Basespace Integration
Sample Tracker Guide
Sample Tracker Guide
What is Sample Tracker?
Project Guide
Project Guide
Create a Project
Navigating a Project
Add a Pipeline to Your Project
Run Guide
Run Guide
What is a Run?
Run Page
Run a Process on Its Own
Sharing a Run
Advance Run Settings
Run Logs
Organizing with Tags
Report Guide
Report Guide
What is a Report?
Visualizing Reports
AI Insights
AI Insight
AI Insight
Overview
Using AI Insight
MCP Server Management
Best Practices and Costs
Troubleshooting
Privacy and Security
Knowledge Builder
Knowledge Builder
Overview
Using Knowledge Builder
Best Practices and Costs
Troubleshooting
Privacy and Security
Cortex
Cortex
What is Cortex?
Using Cortex
Using Foundry Connect with Claude
Using Foundry Connect with Claude
Getting Started
Claude Code
Claude Code in VS Code
claude.ai / Claude for Science
Using Foundry Connect with Copilot, Codex and ChatGPT
Using Foundry Connect with Copilot, Codex and ChatGPT
Getting Started
GitHub Copilot CLI
Copilot in VS Code
Codex CLI
Codex IDE extension
ChatGPT web
App Guide
App Guide
What is an App?
Contextual Apps
Standalone Apps
Workbench Guide
Workbench Guide
What is a Workbench?
Launch a Workbench
Managing your Workbench
Managing Workbench Sessions
Tutorials
Tutorials
Pipeline Tutorials
Pipeline Tutorials
Cellranger
RNA-Seq
Developer Tutorials
Developer Tutorials
Building a Pipeline
App Tutorials
App Tutorials
GSEA Explorer
Network Explorer
Pipeline Specifications
Pipeline Specifications
Metagenomics
Metagenomics
CAMP Pipelines
Foundry Assets
Foundry Assets
Pipelines
Pipelines
ATAC-seq Pipeline
Azimuth Module
Bam Quantification and DE
CellChat2
Cell Ranger ARC
Cell Ranger ATAC Pipeline
Cell Ranger Count Pipeline
Cell Ranger Multi Pipeline
Cell Ranger VDJ Pipeline
Cell Type Mapper (ABA Reference)
CHIP-seq Pipeline
Crispr Screen
DanceMaPper
DE Module
FastQC
Foundry Tutorial Pipeline
GEO Custom Download Module
Germline Variant Calling Pipeline (GATK)
Germline Variant Calling Pipeline from BAM
GSEA Module
HLA Typing
IRFinder Module
LAAVA: Long-read AAV Analysis Pipeline
Liftoff
Meta-CAMP
RiboSeq
RNA-Framework Module
RNA-seq Pipeline
RNA Velocity Module
scRNA-Analysis-Module
scViewer Stork
ShapeMapper2
smallRNA-Seq
Somatic Variant Calling (vs Control) Pipeline
Somatic Variant Calling Pipeline (GATK)
Somatic Variant Calling Pipeline from BAM for RNA-seq
Souporcell Module
Space Ranger Pipeline
Space Ranger with Bin2Cell Segmentation Pipeline
Space Ranger with Segmentation Pipeline
Subclustering Module
TE Transcripts
tRNA-Seq Pipeline
UMInator
Xenium Spatial Analysis Pipeline
Processes
Processes
Alignment
Annotation
Assembly
Binning
Cell Type Mapper
CellChat2
CRISPR
Differential Expression
File Conversions
Functional Profiling
GATK4
Gene Set Enrichment
HLA
Index
IRFinder
LAAVA
MAG-QC
Miscellaneous
Pre-Processing
QC
Ribosome Profiling
Short Read Taxonomy
Single Cell
Spatial
Summary
TE Transcripts
Transcript Quantification
Tutorial
UMInator
Models
Models
Developer Guides
Developer Guides
API Guide
API Guide
API Overview
Personal Access Tokens (PATs)
MCP Integration
Python SDK
Pipeline Guide
Pipeline Guide
Pipeline Basics
Processes
Pipeline Inputs and Configuration
Pipeline Outputs
Import Pipelines
Export Pipelines
Pipeline Settings
Pipeline Versioning
Process Guide
Process Guide
Process Basics
Importing Processes from a Repository
Process Parameters
Process Inputs
Process Outputs
Process Script
Process Options
Testing
Expected Results
Sharing Processes
Advanced Process Topics
App Development Guide
App Development Guide
App Structure
App Dockerfile
Your App in Foundry
Administrator Guide
Administrator Guide
Installation
Configuration
Testing Pipeline
App Section
Browser Support
Backup & Disaster Recovery
Logging
Access Management
Organization Run Environment Connections
OSP Guide
OSP Guide
OSP Sharing Guide
OSP Invitee Guide
Product Updates
Product Updates
What's New
Upgrade Notes
Resources
Resources
Submit a Support Ticket
User FAQ
Developer FAQ
About Us
Cite Us
Privacy Policy
Resources and Support
Submit a Support Ticket
User FAQ
Developer FAQ