* master:
  Bump version number
  Run checks
  Patch fix to lun2Estimate from basics branch
  Update summariseDiff

* devel:

* master:
  Bump version number
  Run checks
  Patch fix to lun2Estimate from basics branch
  Update summariseDiff
  Add counts check to scDDEstimate
  Adjust nEE/nEP estimation
  Update scDD estimation

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131258 bc3139a8-67e5-0310-9ffc-ced21a209358

Import SummarizedExperiment to avoid warnings

* scDD-est:
  Add counts check to scDDEstimate
  Adjust nEE/nEP estimation
  Update scDD estimation

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

* scDD-est:
  Add counts check to scDDEstimate

* 'basics' of github.com:Oshlack/splatter:
  Fix lun2Estimate error

Error when scran::computeSumFactors returns negative values

Error when scran::computeSumFactors returns negative values

* scDD-est:
  Adjust nEE/nEP estimation
  Update scDD estimation

* master:
  Run checks
  Add batch effects to vignette
  Update splatEstimate to set batchCells
  Add batch effects to splatSimulate
  Update SplatParams
  bump x.y.z versions to odd y after creation of 3_5 branch
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel

* devel:
  bump x.y.z versions to odd y after creation of 3_5 branch
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel

* master: (183 commits)
  Run checks
  Add batch effects to vignette
  Update splatEstimate to set batchCells
  Add batch effects to splatSimulate
  Update SplatParams
  Bump version number
  Update citation
  Fix error handling when fitting means
  Fix comparison plots
  Bioconductor 3.5 release
  bump x.y.z versions to odd y after creation of 3_5 branch
  Creating branch for BioC 3.5 release
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Update NEWS and DESCRIPTION
  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@131029 bc3139a8-67e5-0310-9ffc-ced21a209358

* batches:
  Run checks
  Add batch effects to vignette
  Update splatEstimate to set batchCells
  Add batch effects to splatSimulate
  Update SplatParams

* Add batch parameters
* Replace groupCells with group.prob

Now estimates number of each gene type

* release-3.5: