v0.2.0

[mjsteinbaugh]

This is a significant maintenance release designed to simplify the package for
long-term stability. Here we are removing code support for [Seurat][] and
visualization of cell clustering. This functionality has been moved to the new
[pointillism][] package. We have streamlined [bcbioSingleCell][] to simply
import [bcbio][] single-cell data using the bcbioSingleCell() constructor or
[Cell Ranger][] data with the readCellRanger() function. The package continues
to provide quality control visualization (see plotQC()) and low-quality cell
removal with the filterCells() function.

Major changes

• Moved clustering and seurat object support to [pointillism][]:
  cellCountsPerCluster(), cellTypesPerCluster(),
  clusterCellCountsPerSample(), fetchData functions, plotFeature
  functions, plotGene functions, plotMarker functions, plotPCA(),
  plotTSNE(), plotUMAP()`.
• Now requiring [bcbioBase][] v0.4+ and [basejump][] v0.7+.

Defunct functions

• Removed from exports (for simplicifcation): plotClusters(),
  plotFeatures(), quantileHeatmap(), readMarkers(), readMarkersFile().

Minor changes

• No longer exporting mapCellsToSamples(). This is now only called internally.
• Updated documentation to use [roxygen2][] v6.1.

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@cbe02b6). Click here to learn what that means.
The diff coverage is 67.68%.

@@            Coverage Diff            @@
##             master      #77   +/-   ##
=========================================
  Coverage          ?   71.71%           
=========================================
  Files             ?       35           
  Lines             ?     2397           
  Branches          ?        0           
=========================================
  Hits              ?     1719           
  Misses            ?      678           
  Partials          ?        0

Impacted Files	Coverage Δ
R/topBarcodes-methods.R	100% <ø> (ø)
R/barcodeRanksPerSample-methods.R	0% <ø> (ø)
R/AllGenerics.R	75% <ø> (ø)
R/mapCellsToSamples-internal.R	88.88% <ø> (ø)
R/plotUMIsPerCell-methods.R	23.68% <ø> (ø)
R/plotNovelty-methods.R	100% <ø> (ø)
R/plotMitoVsCoding-methods.R	0% <ø> (ø)
R/updateObject-methods.R	0% <ø> (ø)
R/plotGenesPerCell-methods.R	100% <ø> (ø)
R/plotBarcodeRanks-methods.R	0% <ø> (ø)
... and 23 more

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