Chapter 28 Mammary gland dataset

28.1 Introduction

This performs an analysis of the Bach et al. (2017) 10X Genomics dataset, from which we will consider a single sample of epithelial cells from the mouse mammary gland during gestation.

28.2 Analysis code

28.2.5 Variance modelling

We use a Poisson-based technical trend to capture more genuine biological variation in the biological component.

28.2.7 Clustering

We use a higher k to obtain coarser clusters (for use in doubletCluster() later).


Bach, K., S. Pensa, M. Grzelak, J. Hadfield, D. J. Adams, J. C. Marioni, and W. T. Khaled. 2017. “Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.” Nat Commun 8 (1):2128.