Pricing

Free analyses

Paid analysis pricing

What's included

Analyses

Data storage

Downloads

Files with ongoing free storage and downloads

Usage outside the U.S. and Canada

Billing and payments

Contact Cloud Customer Service for help

Billing

10x Genomics Pipeline Runner (formerly known as Cloud Analysis) is a platform for data management, analysis, and collaboration to streamline and accelerate the interpretation of data generated from 10x Genomics assays.

Data analysis,
simplified

Pipeline Runner

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression and multiomic capabilities to profile tens of thousands of cells. Explore cellular heterogeneity, novel targets, and biomarkers with combined gene expression, cell surface protein expression, or CRISPR edits in each cell.

Cell Surface Protein

CRISPR Screening

Sample multiplexing

Reveal the full complexity of cellular diversity, cell by cell

Chromium X Series

Advanced system for multiomic analysis of hundreds to millions of cells.

Single Cell Gene Expression

3' gene expression profiling at scale with single cell resolution.

Formerly known as Cloud Analysis. Analyze 10x Genomics data quickly and securely in the cloud.

Sub-pipeline options by cloud method

Single cell pipeline analysis

Spatial pipeline analysis

Supported pipelines and library types

Web browser app

Command-line interface (CLI)

Prompt-based interface

Supported Products

Supported Pipelines and Products

10x Genomics Pipeline Runner (formerly known as Cloud Analysis) is a platform for data management, analysis, and collaboration to simplify and accelerate the interpretation of 10x Genomics datasets. Pipeline Runner makes it easier than ever to run 10x analysis pipelines and manage your experimental data.

Overview

Tutorials

FAQs

Release Notes

Learn how to create a free account using the two different log-in options.

Account Creation

Tips for deciding which method of running the 10x Cloud best suits your analysis needs.

Choose Cloud Method

Upload input files into your projects using the Web Uploader.

Upload via Web Browser

Upload input files into your projects using the 10x Genomics Cloud CLI.

Upload via CLI

In addition to the pre-built human and mouse reference packages available in Pipeline Runner, you can upload and use your own custom references in your Pipeline Runner projects.

Upload a Reference

After uploading input files into your project in Pipeline Runner, you are ready to analyze your data.

Create Analyses

You are given four unique options for downloading your output files for each completed analysis. These options have certain benefits and limitations that make them appropriate for different circumstances.

Download Output Files

Pipeline Runner allows you to combine data from multiple samples.

Data Integration Workflows

Automatically annotate cell types from Cell Ranger and Cell Ranger ARC outputs.

Cell Annotation Pipeline

The 10x Genomics Cloud CLI is a command line interface (CLI) that allows you to upload input files to projects in your 10x Genomics account, create projects from the command line, and manage other tasks related to your 10x Genomics account.

CLI Documentation

The 10x Genomics Cloud MCP Server enables conversational prompts with AI-powered tools to create single cell analyses.

Prompt-based Interface

Pipeline Runner allows you to transfer projects from your user account to another user account.

Transfer Projects

Copy single cell and spatial data to BioTuring analysis platforms for downstream analysis.

Connect to BioTuring

Pipeline Runner (formerly known as Cloud Analysis) is a platform for data management, analysis, and collaboration to simplify and accelerate the interpretation of supported 10x Genomics single cell and spatial datasets. Pipeline Runner makes it easier than ever to run 10x analysis pipelines and manage your experimental data.

What is Pipeline Runner?

<Text as={'p'} size={'small'} weight={'medium'}><Anchor href={'/support/software/pipeline-runner/latest/tutorials/cloud-bioturing'}>{' Connect'}</Anchor> your 10x Cloud account to BioTuring for an end-to-end workflow that simplifies complex single cell data analysis and exploration. Interact with the 10x Cloud using <Anchor href={'/support/software/pipeline-runner/latest/tutorials/cloud-mcp-server'}>{' conversational prompts'}</Anchor> in Anthropic's Claude Desktop tool!</Text>

After creating a 10x Cloud account, choose how to interact with the Cloud: web browser, command-line, or prompt-based interface.

10x Cloud Methods

Create a project to store your data and analyses. Projects are typically organized by experiment and can contain multiple samples.

Create Projects

Upload input files to your project. Email notifications are available (see notification settings) for job progress updates.

Upload Inputs

Next, select your input files, configure pipeline settings, and create your analysis.

Download analysis outputs to explore your data in Loupe Browser and community-developed tools.

Download Results

Upload custom references, annotate cell types, or run data integration workflows.

Optional Workflow Steps

Find answers to frequently asked questions, including information about browser and operating system support.

We regularly add new features to 10x Genomics Cloud. Find details about the updates and improvements on this page.

Find information about our free usage policies and optional paid services.

Miscellaneous