R code and downstream analysis objects for the scRNA-seq atlas of human breast spanning normal, preneoplastic and tumorigenic states

Chen, Y.; Pal, B.; Lindeman, G. J.; Visvader, J. E.; Smyth, G. K.

doi:10.1101/2021.11.30.470523

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bioRxiv · 10.1101/2021.11.30.470523

R code and downstream analysis objects for the scRNA-seq atlas of human breast spanning normal, preneoplastic and tumorigenic states

Chen, Y.·Pal, B.·Lindeman, G. J.·Visvader, J. E.·Smyth, G. K.

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Abstract

Breast cancer is a common and highly heterogeneous disease. Understanding the cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into the cancer development in human breast. Recently, a large-scale single-cell RNA expression atlas was constructed of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Details of all the bioinformatic analyses that produced the results described in the study are provided.

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Chen, Y., Pal, B., Lindeman, G. J., Visvader, J. E., Smyth, G. K.. 2021-12-01. R code and downstream analysis objects for the scRNA-seq atlas of human breast spanning normal, preneoplastic and tumorigenic states. https://doi.org/10.1101/2021.11.30.470523

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