Chapter 20 Human pancreas dataset (Segerstolpe)

20.1 Introduction

This performs an analysis of the (???) dataset, consisting of human pancreas cells from various donors.

20.2 Analysis code

20.2.4 Quality control

We remove low quality cells that were marked by the authors. We then perform additional quality control, as some of the remaining still have very low counts and numbers of detected features.

20.2.5 Normalization

We don’t normalize the spike-ins as there are some cells with no spike-in counts.

20.2.6 Variance modelling

We do not use cells with no spike-ins for variance modelling. Donor AZ also has very low spike-in counts and is subsequently ignored.

20.3 Results

20.3.4 Dimensionality reduction

## [1] 25

20.3.5 Clustering

## 
##   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18 
## 124 125 104 361 330 137 300 181  68  49  94  39  14  79  42  26  34  17 
##  19 
##  45