Visium kidney cancer dataset at the tumour-normal interface

The kidney cancer dataset profiled by 10x Visium and paired scRNA-seq data [LFL+22] are available to download as h5ad objects in Mendeley Data (https://doi.org/10.17632/g67bkbnhhg.1). We used a sample with the donorid ‘PD47171’ in our analysis.

• Cell type deconvolution using MacSGP
• Applying MacSGP to detect cell-type-specific SGPs
• Kidney cancer dataset analysis
  • Results of RCC
  • Spatial gradient analysis

References

[LFL+22]

Ruoyan Li, John R Ferdinand, Kevin W Loudon, Georgina S Bowyer, Sean Laidlaw, Francesc Muyas, Lira Mamanova, Joana B Neves, Liam Bolt, Eirini S Fasouli, and others. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer cell, 40(12):1583–1599, 2022.