Release Notes Archive

<LinkableSection id={"v1-31"} title={"October 28, 2025"}>

Cell Ranger ARC v2.1 is now live on 10x Cloud Analysis!

</LinkableSection>

<LinkableSection id={"v1-30"} title={"October 20, 2025"}>

Users can now interact with the 10x Cloud using conversational prompts in Anthropic's Claude Desktop and Claude Code tools! See [this page](/support/software/cloud-analysis/latest/tutorials/cloud-mcp-server) for details.

Refer to the [supported pipelines and products page](/support/software/cloud-analysis/latest/miscellaneous/CA-supported-products) for full details on prompt-based 10x Cloud support.

</LinkableSection>

<LinkableSection id={"v1-29"} title={"October 16, 2025"}>

The 10x Genomics Cloud TXG CLI has been updated to v4.0.0. You can now create, cancel, or delete analyses, specify files, and run batch analyses from the command line. See the instructions for [Linux](/support/software/cloud-analysis/latest/tutorials/CA-cloud-cli-documentation-for-linux), [Mac](/support/software/cloud-analysis/latest/tutorials/CA-cloud-cli-documentation-for-mac), or [Windows](/support/software/cloud-analysis/latest/tutorials/CA-cloud-cli-documentation-for-windows) for more details.

A different subset of 10x pipelines are supported in the CLI than in the web browser. The [supported pipelines and products](/support/software/cloud-analysis/latest/miscellaneous/CA-supported-products) page has been updated to reflect this.

</LinkableSection>

<LinkableSection id={"v1-28"} title={"August 18, 2025"}>

[Space Ranger 4.0.1](/support/software/space-ranger/latest/release-notes/release-notes-for-SR) is now available on Cloud Analysis to support Visium HD 3' Gene Expression and cell segmentation. Custom segmentation masks are not supported on Cloud Analysis.

</LinkableSection>

<LinkableSection id={"v1-24"} title={"June 9, 2025"}>

Cloud Analysis introduces a new data integration workflow that employs SCTransform and Harmony to integrate data from multiple samples. See the [Create Analyses](/support/software/cloud-analysis/latest/tutorials/CA-creating-analyses#norm-batch-corr) and [Normalization and Batch Correction](/support/software/cloud-analysis/latest/tutorials/CA-normalization-batch-correction) pages for details and usage guidance.

</LinkableSection>

<LinkableSection id={"v1-27"} title={"April 8, 2025"}>

TXG CLI v3.0.1 has been released in order to resolve an issue where file upload would fail for Windows devices.

</LinkableSection>

<LinkableSection id={"v1-26"} title={"April 7, 2025"}>

Cloud Analysis now offers the flexibility to analyze Flex libraries with or without a transcriptome reference.

</LinkableSection>

<LinkableSection id={"v1-25"} title={"March 25, 2025"}>

The analysis of Multiplex Flex CRISPR is now available with Cell Ranger v9.0.1 on Cloud Analysis.

The `emptydrops_min_umis` parameter in the `cellranger multi` pipeline is now available for Flex libraries with Cell Ranger v9.0.1.

Human and mouse 2024-A transcriptome references for Cell Ranger ARC are now accessible on Cloud Analysis.

When selecting libraries in Cloud Analysis, the on-chip multiplexing (OCM) library is now labeled with "OCM" in its name.

</LinkableSection>

<LinkableSection id={"v1-23"} title={"March 11, 2025"}>

The analysis of Universal Gene Expression samples hashed with Antibody Capture is now available with Cell Ranger v9.0.1 on Cloud Analysis.

The `enable-tsne` parameter in the `cellranger aggr` pipeline is now available with Cell Ranger v9.0.1.

The Cloud Analysis UI has been updated to improve navigation in projects of over 100 FASTQ files. If you encounter any issues while sorting or assigning libraries, please refresh your browser.

</LinkableSection>

<LinkableSection id={"v1-22"} title={"February 26, 2025"}>

The analysis of Universal Gene Expression + CRISPR Guide Capture libraries with on-chip multiplexing (OCM) is now available with Cell Ranger v9.0.1 on Cloud Analysis.

Support for analyzing libraries hashed with Antibody Capture is coming soon.

</LinkableSection>

<LinkableSection id={"v1-21"} title={"February 19, 2025"}>

[Space Ranger 3.1.3](/support/software/space-ranger/latest/release-notes/release-notes-for-SR) is now available on Cloud Analysis to support Visium HD Spatial Gene Expression (Visium v1/v2 are not supported).

The 10x Genomics prebuilt [_Rattus norvegicus_ transcriptome reference](/support/software/cell-ranger/downloads#reference-downloads) is now available for use with Cell Ranger v9.0.0 (and later) on Cloud Analysis.

</LinkableSection>

<LinkableSection id={"v1-20-3"} title={"February 11, 2025"}>

GEM-X on-chip multiplexing (OCM) is now available on Cloud Analysis with Cell Ranger v9.0.

Known issue: GEM-X CRISPR Guide Capture analysis with sample multiplexing is not yet enabled in v9.0 (coming soon).

</LinkableSection>

<LinkableSection id={"archive"} title={"Archive"}>

<Flex style={{
 flexDirection: "column",
 gap: "18px",
 padding: "1rem 0 2rem 0"
}}>
<WorkflowCard link={"/support/software/cloud-analysis/latest/release-notes/CA-release-notes-archive"} title={"Archive"} subtext={"Access release notes for past versions of Cloud Analysis."} />
</Flex>

</LinkableSection>

Recent Updates

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

Overview

Supported Products

Tutorials

FAQs

Release Notes

Billing

Cloud Analysis

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

Account Creation

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 Cloud Analysis, you can upload and use your own custom references in your Cloud Analysis projects.

Upload a Reference

After uploading input files into your project in Cloud Analysis, 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

Cloud Analysis allows you to combine data from multiple samples.

Data Integration Workflows

Cloud Analysis allows you to transfer projects from your user account to another user account.

Transfer Projects

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

10x Genomics 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. Cloud Analysis makes it easier than ever to run 10x analysis pipelines and manage your experimental data.

What is Cloud Analysis?

<Text as={'p'} size={'small'} weight={'medium'}>Interact with the 10x Cloud using <Anchor href={'/support/software/cloud-analysis/latest/tutorials/cloud-mcp-server'}>{' conversational prompts'}</Anchor> in Anthropic's Claude Desktop tool! If you are a member of a core lab or service provider, see <Anchor href={'/support/software/cloud-analysis/latest/getting-started/CA-guidance-for-cores'}>{'how Cloud Analysis can help improve your workflow'}</Anchor>. Explore the <Anchor href={'/support/software/cloud-analysis/latest/tutorials/CA-normalization-batch-correction'}>{'SCTransform/Harmony data integration workflow'}</Anchor> and the <Anchor href={'/support/software/cloud-analysis/latest/tutorials/CA-cell-annotation-pipeline'}>{'beta pipeline for generating cell type annotations'}</Anchor>.</Text>

Projects are where you upload data and run analysis pipelines. People typically create projects for each experiment. You can upload different samples to a single project.

Create Projects

Upload input files either directly from your web browser or via the 10x Genomics Cloud CLI.

Upload input files

After uploading, select the file sets that you want to work with. Then configure your pipeline settings and start the analysis.

You can optionally receive an email when your analysis completes. When your results are ready, you can download the analysis outputs and explore your data using Loupe Browser or a variety of community-developed tools.

Download Results

10x Genomics pre-built human, mouse, and barnyard references are available. You may optionally upload your own custom references to use in the analyses on your account.

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.