I went through the book and fixed some typos :)
A couple of additional comments:
[ ] In the infrastructure chapter (4.2.2/4.4), it is indicated that reducedDims() and assays() show the names of the reduced dims/assays, which they of course do, but if one only wants the names one could use reducedDimNames() and assayNames().
[ ] The infrastructure chapter (4.3) says that sizeFactors is defined in SummarizedExperiment, but iirc it is from SingleCellExperiment.
[ ] Section 4.4 says that scater uses the umap package, but I think it already uses uwot.
[ ] The figure in section 4.8 doesn't show the things that are indicated in the legend.
[ ] There's some strange text in the bottom of chapter 4, and no session info.
[ ] Some deprecated/not actually used functions are mentioned in the text: spikeNames(), isSpike(), scater::normalize() (section 10.3), overlapExprs() and pairwiseBinom() (section 11.3)
I went through the book and fixed some typos :) A couple of additional comments:
reducedDims()
andassays()
show the names of the reduced dims/assays, which they of course do, but if one only wants the names one could usereducedDimNames()
andassayNames()
.sizeFactors
is defined inSummarizedExperiment
, but iirc it is fromSingleCellExperiment
.scater
uses theumap
package, but I think it already usesuwot
.spikeNames()
,isSpike()
,scater::normalize()
(section 10.3),overlapExprs()
andpairwiseBinom()
(section 11.3)