Still some warnings from BASiCS...

Split into functions, can now actually tell how it works...

Fix spelling

Fixes #64

Also remove lingering references to phenoData and featureData

* master:
  Change mean-dropout to mean-zeros
  Add verbose to scDDEstimate

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131415 bc3139a8-67e5-0310-9ffc-ced21a209358

* 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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131258 bc3139a8-67e5-0310-9ffc-ced21a209358

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

* 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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131029 bc3139a8-67e5-0310-9ffc-ced21a209358

* 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: file:///home/git/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

* 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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127789 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 0.99.12
  Run checks
  Warn if bcv.df is infinite
  Update addFeatureStats col names
  Update progress message
  Switch to boxplots in compareSCESets
  Change Lun2 nGenes estimate
  Add diffSCESets to vignette
  Add diffSCESets function

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127605 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.12
  Run checks
  Warn if bcv.df is infinite
  Update addFeatureStats col names
  Update progress message
  Switch to boxplots in compareSCESets
  Change Lun2 nGenes estimate
  Add diffSCESets to vignette
  Add diffSCESets function

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127605 bc3139a8-67e5-0310-9ffc-ced21a209358

Make it clear which are added by Splatter