* 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

* 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:

* master:
  Bump version number

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129893 bc3139a8-67e5-0310-9ffc-ced21a209358

* release-3.5:

* master:
  Update citation

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129821 bc3139a8-67e5-0310-9ffc-ced21a209358

* release-3.5:

* master:
  Fix error handling when fitting means

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129584 bc3139a8-67e5-0310-9ffc-ced21a209358

* release-3.5:
  Creating branch for BioC 3.5 release

* master: (175 commits)
  Fix comparison plots
  Bioconductor 3.5 release
  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
  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
  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
  Version 0.99.13
  ...

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129246 bc3139a8-67e5-0310-9ffc-ced21a209358

* 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

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

* devel:

* master:
  Update NEWS and DESCRIPTION

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129048 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Update NEWS and DESCRIPTION

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@129048 bc3139a8-67e5-0310-9ffc-ced21a209358

* devel:

* 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 0.99.15
  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