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Space Ranger
Introduction
What is Space Ranger?
Direct placement for FF
Direct placement for FFPE
CytAssist enabled workflow
What is Targeted GEX?
Glossary
Downloads
Download Links
System Requirements
Installing Space Ranger
Release Notes
Tutorials
Getting Started
Setup Spaceranger
count for FF
count for FFPE
count for CytAssist TMA
Running Pipelines
Choosing Pipelines
Computing Options
Input FASTQs
Sequencing Recommendations
Generating FASTQs
Specifying Input FASTQs
Input Image
Image Recommendations
Slide Parameters
Slide Layout Download
Fiducial Alignment
CytAssist Image Alignment
Poly-A Based Assay
Spatial GEX (count)
Targeted GEX (count)
targeted-compare
targeted-depth
aggr
Probe-based Assay
Spatial GEX (count)
CytAssist GEX (count)
aggr
Troubleshooting
Understanding Outputs
Overview
Web Summary
Analysis
Matrices
Spatial
BAM
Molecule Info (H5)
Spatial GEX Outputs
Outputs Overview
GEX Metrics
Targeted GEX Outputs
Outputs Overview
Targeted-Compare
Aggregate Outputs
Outputs Overview
Web Summary
Aggregate Metrics
Algorithms Overview
Image Processing
Gene Expression
Targeted GEX
Advanced
Matrix HDF5 Format
Job Submission Mode
Cluster Mode
Demultiplexing with Illumina Software
Custom References
Pipeline Monitoring UI
Pipestance Structure
Loupe
Introduction
What is Loupe Browser?
Release Notes
Download
Tutorials
Overview
Navigation
Evaluate Gene Markers
Explore Spatial Clusters
Characterize Substructure
Spatial Reclustering
Sharing Results
Fiducial Alignment
CytAssist Image Alignment
10x Genomics
Spatial Gene Expression
Space Ranger, printed on 12/26/2024
Release Notes for Space Ranger 1.0.0
Initial release.
