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Cell Ranger
Cell Ranger Datasets
Cell Ranger
Overview
Getting Started
Supported Libraries
Download Center
Cloud Analysis
Cell Ranger Commands
Analysis
Inputs
List of Inputs
Generating FASTQs
Specifying FASTQs
Libraries CSV
Feature Reference CSV
Multi Config CSV
Custom Reference with mkref
Custom V(D)J Reference
Running Pipelines
Choosing a pipeline
Primary Analysis
multi (3'/5'/Flex)
count (GEX + Antibody/CRISPR)
vdj (VDJ-T/B only)
Secondary Analysis
Aggregate Multiple Samples (aggr)
Cell Annotation (annotate)
Custom Analysis (reanalyze)
Outputs
Outputs by pipeline
Web Summary
Metrics
Feature-Barcode Matrices
BAM
Molecule Info (H5)
Secondary Analysis
Results of aggr
Library types
Gene Expression
Antibody Capture
CRISPR Guide Capture
VDJ-T/B
3'/5' Singleplex (GEX + VDJ + FB)
3'/5' Sample Multiplexing (GEX + VDJ + FB)
Flex (Singleplex & Multiplex)
Tutorials
Algorithms
Advanced
Troubleshooting
Miscellaneous
Release Notes
Q&A
Glossary
Datasets
Loupe Browser
Version
v9.0 (Latest)
View source code
Cell Ranger Datasets
Datasets by product
3' Single Cell Gene Expression
5' Immune Profiling
Flex
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Datasets by product