Single Cell Analysis

A whole new visual canvas to explore single cell data

Download Loupe
Download Loupe V(D)J
Visium breast cancer sample data

Your roadmap to single cell data analysis

Our software tools make processing, visualizing, and exploring your single cell data easy, even without bioinformatics help.

Chromium analysis single cell
Cell Ranger analysis pipelines

Transform raw sequences into single cell insights

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell data.

View Cell Ranger documentation
    Alignment layer

    Start with Cell Ranger to align reads, generate cell-feature matrices, perform clustering and secondary analysis

    Cell Ranger can process raw sequencing data, perform QC, identify cell barcodes, and quantify gene expression levels at the single cell level.

    Alignment layer

    Accelerate your time to results with Cloud Analysis, a web app for running Cell Ranger

    Access Cell Ranger from your web browser with Cloud Analysis.

Loupe Browser

10 ways to dig into your data with Loupe Browser

Loupe Browser is a desktop application for Windows and MacOS that allows you to interactively visualize data.


Use Loupe to dive deeper into your Seurat analysis, no code required

LoupeR is an R package that creates a Loupe Browser file from a Seurat object.

With LoupeR, seamlessly explore Seurat data in Loupe without command-line data wrangling.


Find differentially expressed genes in treatment vs. control experiments

Easily perform and iterate on multi-sample comparisons.


Rapidly visualize expression of your favorite genes


Quickly plot your differential expression results

Explore interactive heat maps and violin plots of differentially expressed genes.


Easily annotate cell types

Start from scratch or refine existing cell types.


Generate fast and interactive differential expression analyses


Reanalyze subsets of data to find new cell types

Narrow in on your cell types of interest or filter out low quality data.


Create high-resolution figures in a few clicks

Loupe Browser makes it easy to generate SVG and PNG formatted images to share in presentations or publications.


Characterize cells using advanced filters

Hone in on particular sets of barcodes by creating a custom set of rules with boolean operators.


Explore many modalities of data, including single cell V(D)J, ATAC, and spatial gene expression

Loupe Browser supports the full suite of 10x Genomics single cell and spatial datasets.

Explore single cell data

Download diverse 10x Genomics datasets with various assays, samples, and species.

  • image

    Aggregate of ~900k Human Non Small Cell Lung Cancer and Normal Adjacent Cells

    Number of cells
  • image

    Alzheimer's Disease Mouse Model - Brain Coronal Sections from One Hemisphere Over a Time Course

    Number of cells

Explore datasets, documentation and tutorials