* scDD-update:
  Run checks
  Update scDDEstimate
  Update SCDDParams
  Update scDDSimulate

* SCE:
  Build pkgdown
  Run checks
  Update README
  Update vignette to SCE
  Fix error in simulating batches
  Switch to BiocGenerics::counts
  Update SCE and comparison functions
  Fix accessing counts
  Update simulation documentation
  Convert simulations to SingleCellExperiment

Problem using factor to index matrix

* upstream/master:
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into 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
  Adding goSTAG, splatter, karyoploteR, discordant, POST, MCbiclust

* 'master' of github.com:Oshlack/splatter:

Add pkgdown site

* pkgdown:
  Add extra.css
  Add index.md
  Add reference index
  Add _pkgdown.yml
  Add basic site

* devel:

* master:
  Fix group factors bug

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131740 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Fix group factors bug

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131740 bc3139a8-67e5-0310-9ffc-ced21a209358

* devel:

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

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

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

* scDD-est:
  Change mean-dropout to mean-zeros
  Add verbose to scDDEstimate

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

* 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

* 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