Sub-sampled 10x Xenium breast cancer (IDC) spatial transcriptomics dataset

A 10x Xenium spatial transcriptomics dataset containing a sub-region of a intra-ductal carcinoma (IDC) breast cancer sample. The data contains pathology annotations. The full dataset is available through the SubcellularSpatialData R/Bioconductor package.

idc

Format

A SpatialExperiment object.

References

Bhuva DD, Tan CW, Salim A, Marceaux C, Pickering MA, Chen J, Kharbanda M, Jin X, Liu N, Feher K, Putri G. Library size confounds biology in spatial transcriptomics data. Genome Biology. 2024 Apr 18;25(1):99.

Bhuva DD, Tan CW, Marceaux C, Pickering M, Salim A, Chen J, Kharbanda M, Jin X, Liu N, Feher K, et al. Library size confounds biology in spatial transcriptomics data. 2024. Zenodo. https://doi.org/10.5281/zenodo.7959786.

Bhuva DD: SubcellularSpatialData: annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. Bioconductor. 2024 https://doi.org/10.18129/B9.bioc.SubcellularSpatialData.

Bhuva DD. Library size confounds biology in spatial transcriptomics. 2024. Zenodo. https://doi.org/10.5281/zenodo.10946961.