A preview of STHDviewer for spot-level cell typing for a human colon cancer VisiumHD data.

• The webpage can be viewered at https://yi-zhang-compbio-lab.github.io/STHDviewer_colon_cancer_hd/STHDviewer_crchd.html.
• The html can be rendered on website or downloaded and hosted in web browsers.
• Generated by Bokeh. Chrome is recommended. Takes ~10s for rendering.

Generated by STHD software in development

• STHD git repo

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Data acknowledgement

• scRNA reference: The reference scRNA-seq atlas data and cell type annotation from Human Colon Cancer Atlas was downloaded from Pelka et. al through GSE178341: (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178341).
• VisiumHD data from 10X Genomics: We downloaded the publicly available VisiumHD data demonstrated at https://www.10xgenomics.com/support/software/loupe-browser/latest/tutorials/assay-analysis/lb-hd-spatial-gene-expression from https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc, named Visium HD Spatial Gene Expression Library, Human Colorectal Cancer (FFPE), by Space Ranger 3.0.0, 10x Genomics (2024, Mar 25).

Preprint

• BioRxiv link available soon