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Space Ranger

Space Ranger

software-intro
What is Space Ranger?

Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map the whole transcriptome in a variety of tissues. Space Ranger v4.0 now supports Visium HD 3'.

Download Space RangerUse Cloud AnalysisGet Started with Space Ranger
Starting with v4.0, anonymized telemetry data is collected and sent to 10x Genomics. Learn how to disable.

The spaceranger mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate Space Ranger-compatible FASTQ files.

Analysis

Inputs

Learn about input files required to run Space Ranger

Running Pipelines

Learn how to run Space Ranger

Outputs

Learn about the output files generated by Space Ranger

Tutorials

Set up Space Ranger
Install Space Ranger and perform a test run
Space Ranger for FF
Learn how to analyze fresh frozen (FF) samples with spaceranger count
Space Ranger for FFPE
Learn how to analyze formalin fixed paraffin embedded (FFPE) samples with spaceranger count
View all tutorials

Algorithms overview

Overview of algorithms

Advanced

Advanced pipeline content for Space Ranger

Release Notes

View the latest updates to Space Ranger

Q&A

Browse Q&As from the 10x Genomics support team

Datasets

Access free public Visium data from 10x Genomics

Analysis Guides

A collection of introductions, tutorials, and blogs for data analysis beyond software

Loupe Browser

Loupe Browser is a desktop application for interactive data visualization