Cell Ranger ARC v2.1 is now live on 10x Cloud Analysis!
Users can now interact with the 10x Cloud using conversational prompts in Anthropic's Claude Desktop tool! See this page for details.
Refer to the supported pipelines and products page for full details on prompt-based 10x Cloud support.
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, Mac, or 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 page has been updated to reflect this.
Space Ranger 4.0.1 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.
Cloud Analysis introduces a new data integration workflow that employs SCTransform and Harmony to integrate data from multiple samples. See the Create Analyses and Normalization and Batch Correction pages for details and usage guidance.
TXG CLI v3.0.1 has been released in order to resolve an issue where file upload would fail for Windows devices.
Cloud Analysis now offers the flexibility to analyze Flex libraries with or without a transcriptome reference.
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.
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.
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.
Space Ranger 3.1.3 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 is now available for use with Cell Ranger v9.0.0 (and later) on Cloud Analysis.
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).