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Space Ranger

Introduction

What is Space Ranger?
Glossary

Downloads

Download Links
System Requirements
Installing Space Ranger
Release Notes

Running Pipelines

Computing Options
Input Recommendations
mkfastq
Specifying Input FASTQs
count (Spatial Gene Expression)
Troubleshooting

Understanding Outputs

Overview
Web Summary
Analysis
Matrices
Images
BAM
Molecule Info (H5)
GEX/Image Metrics

Algorithms Overview

Image Processing
Gene Expression
Map of count Pipeline

Advanced

Matrix HDF5 Format
Job Submission Mode
Cluster Mode
Using bcl2fastq
Custom References
Pipeline Monitoring UI
Pipestance Structure
Secondary Analysis in R

Loupe

Introduction

What is Loupe Browser?

Download

Download Link
Installing Loupe Browser

Tutorials

Navigation
Spatial Gene Expression
Manual Alignment

10x Genomics
Visium Spatial Gene Expression

Space Ranger1.0, printed on 11/22/2024

Release Notes for Space Ranger 1.0.0

Initial release.

1.1
1.2
1.3
2.0 (latest)
Space Ranger v1.0

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