Case Study: Macaulay & Svensson, Cell Reports (2016)

Olga: print this paper for people to have

This "Case Study" is somewhat like a journal club except instead of just presenting the paper, we're going to re-work through some of these analyses ourselves and see how the interpretation of the data changes by using different algorithms

We will be using In this paper, co-authors Macaulay and Svensson studied haematopoesis in Zebrafish by doing...

Clustered cells into groups (Figure 1)
Ordered them by psuedotime (Figure 2)
Showed expression of known (Figure 3) and novel (Figure 4) lineage markers
Found a novel early committed group in the kidney before circulation in the blood (Figure 5)
Identified genes that were differentially regulated over pseudotime (Figure 6)
Investigated usage of duplicated genes during thrombopoeisis (Figure 7)

The computational scientist, Valentine Svensson, kindly provided the notebooks and analyses on GitHub, and the exercises today are adapted from them. We're going to follow along, playing with different parameters as much as we can, until it gets to the very domain-specific analyses. The full set of notebooks are here: