
Loupe Browser uses the same underlying algorithms as Cell Ranger for its core analyses, providing a consistent framework for data exploration.

For detailed information on specific methods, refer to the corresponding sections on the [Cell Ranger Algorithms](/software/cell-ranger/latest/algorithms-overview) page.

### Clustering (graph based and k means)

Loupe Browser employs graph-based and k-means clustering to group cells with similar gene expression profiles, enabling the identification of distinct cell populations within your data.

[Relevant Cell Ranger Algorithms Link](/support/software/cell-ranger/latest/algorithms-overview/cr-gex-algorithm#clustering)

### Differential gene expression

Loupe Browser compares average gene expression between cell groups using the exact negative binomial test, switching to the faster edgeR asymptotic test for large counts.

[Relevant Cell Ranger Algorithms Link](/support/software/cell-ranger/latest/algorithms-overview/cr-gex-algorithm#diffexp)

### Multi-sample comparison

Loupe Browser (v7.0 and later) enables differential expression within cell types and between experimental conditions with multi-sample comparison (aka pseudo-bulk)

To test for differences in mean expression between groups of cells within a cell type, Loupe Browser first reads the entire gene expression count matrices from Cell Ranger. For every cluster (cell type), a new matrix is generated in which each column is the sum of all barcodes in that sample within the selected cluster (cell type). Loupe Browser then applies the exact negative binomial test proposed by the authors of the sSeq method (Yu, Huber, & Vitek, 2013) to the condensed sample matrices to test for significant differences.

Loupe Browser's implementation differs slightly from the original sSeq method in its normalization approach. Instead of using DESeq's geometric mean for library size, Loupe Browser calculates size factors based on the total UMI count per sample. Similar to sSeq, normalization is implicitly handled by incorporating these per-sample size factors into the probability calculations.


Loupe Browser algorithms for Universal 3', 5', and Flex datasets

Universal 3', 5', Flex Algorithms

Loupe Browser is a powerful visualization software that provides intuitive analysis functionality you need to explore your 10x Genomics data.

Overview

Getting Started

Download Center

Tutorials

Algorithms

Release Notes

Loupe V(D)J Browser

Datasets

Analysis Guides

Loupe Browser

Learn about Loupe Browser and get oriented with its interface and features.

Introduction

Navigation for Single Cell Gene Expression

Navigation for Spatial Gene Expression

LoupeR is an R package developed by 10x Genomics that works with Seurat objects to create a Loupe Browser file.

LoupeR

Learn about product-specific analysis capabilities to quickly gain insights from your 10x data.

Assay Analysis

New Tutorial: Mapping the Tumor Microenvironment with Visium HD

HD Spatial Gene Expression

Spatial Gene Expression (v1/v2)

Single Cell Gene Expression & Flex

Single Cell Immune Profiling

Single Cell ATAC

Single Cell Multiome ATAC + Gene Expression

Visium Manual Alignment

Identify fiducials, perform tissue selection and align CytAssist and microscope images for Visium HD. You will then export a JSON file for Space Ranger analysis.

Visium HD manual alignment

Manually identify the fiducials in your Visium image and select spots under tissue. You will then export a JSON file for Space Ranger analysis.

Manual Fiducial Alignment and Tissue Detection (Visium v1/v2)

Align your CytAssist image and microscope image. After you complete this step, you can either export a JSON file for Space Ranger automated fiducial and tissue detection, or continue to Visium Fiducial Alignment.

Manual CytAssist Image - Microscope Image Alignment (Visium v1/v2)

Visium manual alignment for Space Ranger

Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze your 10x Genomics Chromium and Visium data. You can also convert your Seurat objects into Loupe Browser files using the LoupeR package.

What is Loupe Browser?

<Text as={'p'} size={'large'} weight={'medium'}>Loupe Browser v9.0 is now available!</Text>

Algorithms overview

View the latest updates to Loupe Browser.

Browse Q&As from the 10x Genomics support team.

Access free, publicly available data from 10x Genomics.

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

Algorithms Overview