10x Genomics Support/Space Ranger/Analysis/

Run spaceranger count

The spaceranger count pipeline is compatible with most Visium data, including Visium HD. The pipeline inputs a reference, a microscope slide image, and FASTQ files to generate feature-barcode matrices, identify clusters, and perform differential gene expression.

Count for Visium HD Spatial Gene Expression

For FFPE tissues prepared with the Visium CytAssist.