Add more Seurat functions?

[mblue9]

Thanks for adding your scripts to Bioconda!

I'm wondering if these other Seurat functions should have wrappers here?

These are the functions (mainly visualisation) that I'd already included in the current Galaxy Seurat tool based on the Seurat Guided Clustering tutorial:

• VlnPlot
• GenePlot
• VizPCA
• PCAPlot
• PCHeatmap
• JackStraw
• JackStrawPlot
• PCElbowPlot
• TSNEPlot
• FindAllMarkers
• DoHeatmap

And these are the functions I was working on adding here, based on the Seurat integration of 2 groups tutorial:

• RunCCA
• MetageneBicorPlot
• DimHeatmap
• CalcVarExpRatio
• SubsetData
• AlignSubspace
• RunMultiCCA

[pinin4fjords]

Hi @mblue9 . Yep, I had just started with the core components of what I considered the 'core' Seurat workflow, with the intent to flesh out later. My priority was analysis rather than visualisation, hence the lack of those routines.

We're trying to keep to one function per script so the components can be linked together in a variety of workflows (Galaxy and otherwise).

Automating this as you suggest in galaxyproject/tools-iuc#2047 (comment), either via r2g2 or an approach inspired by it, would seem to be the sensible way to go, will look into it.