Version 1.3.0

Changed

• Moved some code to the new package sccore
• Fixed inconsistent use of parameters for different spaces in buildGraph
• Various small fixes
• Fixed the number of components calculated for the simple PCA rotation
• Conos is R6 class now (instead of refClass)

Added

• Functionality for PAGA graph collapsing
• Parameters k.same.factor and balancing.factor.per.sample to buildGraph.
  It can be used to improve alignment between different conditions: with same.factor.downweight
  it gives the system similar to k.self and k.self.weight
• plotDEheatmap() function for viewing marker genes
• Function convertToPagoda2 to create Pagoda 2 from Conos. Helpful for PagodaWebApp.