* diff:
  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

Make it clear which are added by Splatter

Drawing quantiles in violins was causing an error

No gives the number of rows in the original counts

* devel:

* master:
  Version 0.99.11
  Run checks
  Fix mean-zeros scale
  Make lun2Estimate parallel
  Allow non-interger Lun 2 lib sizes
  Fix dropout eta

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127511 bc3139a8-67e5-0310-9ffc-ced21a209358

* lun2-update:
  Run checks
  Fix mean-zeros scale
  Make lun2Estimate parallel
  Allow non-interger Lun 2 lib sizes
  Fix dropout eta

Adjust point size

For compatibility with pseudo-counts

Remove cell component

* devel:

* master:
  Version 0.99.10
  Remove out.loProb from vignette
  Update default Splat parameters
  Remove out.loProb parameter
  Update estimation procedure

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127213 bc3139a8-67e5-0310-9ffc-ced21a209358

* est:
  Remove out.loProb from vignette
  Update default Splat parameters
  Remove out.loProb parameter
  Update estimation procedure

Decided it was unnecessary

* Winsorize means
* Only high outliers
* Scale edgeR dispersion

* devel:

* 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

* length:
  Update scDD reference
  Add addGeneLengths to vignette
  Add addGeneLengths tests
  Add addGeneLengths function
  Update Roxygen version

* devel:
  Adding goSTAG, splatter, karyoploteR, discordant, POST, MCbiclust

* 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