New things

[wikiselev]

1. Imputation chapter
2. Separate chapter for SEURAT
3. Add more better batch correction methods
   (optional) 4. Cross-dataset comparison (scmap, metaneighbour, mnnCorrect, CCA-part of Seurat)

[mhemberg]

1. Magic and scImpute (and maybe more) (Martin)
2. Adapt one of their tutorials. Do clustering for small and large datasets. (Vlad)
3. Discuss batch correction methods (Tallulah)
4. Cross-dataset comparisons (Vlad)
5. Introduction to BioConductor classes (Davies)

[mhemberg]

3. Internal batch correction (as before) AND Compare across datasets
4. Mapping/projection

[tallulandrews]

Shall we remove the edgeR DE stuff from the counfounders chapter? It isn't very useful & somewhat off-topic.

[wikiselev]

Yes, I agree, please feel free to do it. I have updated everything until clustering chapters. Hopefully will be able to build the new version tomorrow, will let you know.

[wikiselev]

I have removed DE stuff from confounders chapter

[tallulandrews]

To myself - may need to sort assayNames to make figures more interpret-able. & check how bit a mess it is with the millions of figures....