* 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

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

* master:
  Bump version number
  Update scDD reference
  Add addGeneLengths to vignette
  Add addGeneLengths tests
  Add addGeneLengths function
  Update Roxygen version
  Update README
  Add bioc-devel to Travis

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126415 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Bump version number
  Update scDD reference
  Add addGeneLengths to vignette
  Add addGeneLengths tests
  Add addGeneLengths function
  Update Roxygen version
  Update README
  Add bioc-devel to Travis

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126415 bc3139a8-67e5-0310-9ffc-ced21a209358

* master: (123 commits)
  Fix non-linear path factors
  Bump verison number
  Set some examples to not run to save check time
  Initalise scDatEx to avoid NOTE
  Tidy up and bump version
  Replace 1:x
  Remove splatter.Rproj
  Add more detail about counts matrix
  Add installation to vignette
  Set R_TESTS environment
  Bump version to start build
  splatter 0.99.3
  Updata scDDEstimate
  Add condition parameter
  Modify SCDDParams to take SummarizedExperiment
  Add logo to vignettes directory
  Remove scDD github remote
  Update to R-devel
  Address Bioconductor build warnings, notes
  Prepare for Bioconductor submission
  ...

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358

* master: (123 commits)
  Fix non-linear path factors
  Bump verison number
  Set some examples to not run to save check time
  Initalise scDatEx to avoid NOTE
  Tidy up and bump version
  Replace 1:x
  Remove splatter.Rproj
  Add more detail about counts matrix
  Add installation to vignette
  Set R_TESTS environment
  Bump version to start build
  splatter 0.99.3
  Updata scDDEstimate
  Add condition parameter
  Modify SCDDParams to take SummarizedExperiment
  Add logo to vignettes directory
  Remove scDD github remote
  Update to R-devel
  Address Bioconductor build warnings, notes
  Prepare for Bioconductor submission
  ...

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358

Fix bug that meant non-linear path factors weren't stored in output of
splatSimulatePaths

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@125902 bc3139a8-67e5-0310-9ffc-ced21a209358

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@125902 bc3139a8-67e5-0310-9ffc-ced21a209358

* Add locfit to NAMESPACE
* Add return values to logistic, showPP documentation
* Delete commented mergeParams function
* Switch to aes_string in compareSCESets
* Add examples to getParam, setParam
* Adjust line lengths
* Adjust indentation