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Cell Ranger
Getting Started
Cell Ranger Datasets
Cell Ranger
Overview
Getting Started
Supported Libraries
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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
Library types
GEX + Antibody/CRISPR (count)
VDJ-T/B only (vdj)
3'/5' Sample Multiplexing (multi)
VDJ + GEX + Antibody/CRISPR/BEAM (multi)
Flex (multi)
Secondary Analysis
Aggregate Multiple Samples (aggr)
Cell Annotation (annotate)
Custom Analysis (reanalyze)
Outputs
Overview
Web Summary
Metrics
Feature-Barcode Matrices
BAM
Molecule Info (H5)
Secondary Analysis
Results of aggr
Library types
Gene Expression
Antibody Capture
CRISPR Guide Capture
Sample Multiplexing
VDJ-T/B
VDJ + GEX + BEAM
Flex
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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