Problem using factor to index matrix

Import SummarizedExperiment to avoid warnings

* Add MAE, RMSE
* Add scaled stats
* Add ranks
* Only return long table

* Add batch parameters
* Replace groupCells with group.prob

Now estimates number of each gene type

* Fix scale in zeros diff plots
* Fix diff plot colours
* Fix panel legends

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129128 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.15
  Remove dropout.present estimation
  Add limits to zeros plots
  Adjust default splat DE fac params
  Add BPPARAM to scDDSimulate
  Add summariseDiff function

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@128698 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.14
  Add panel function to vignette
  Change var plot scale
  Run checks
  Update panel functions
  Add makeOverallPanel function
  Add makeDiffPanel function
  Add options to comparison plots

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127789 bc3139a8-67e5-0310-9ffc-ced21a209358

For consistency

* master:
  Version 0.99.13
  Run checks
  Update Lun2 documentation
  Modify Lun2Params to use data.frame

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127694 bc3139a8-67e5-0310-9ffc-ced21a209358