NEWS.md

1.1.4

• Fix group factors bug

1.1.3

• Add verbose option to scDDEstimate
• Change "mean-dropout" to "mean-zeros" in compareSCESets

1.1.2

• Update summariseDiff
• Update scDDEstimate, now estimates gene types
• Fix error in lun2Estimate
• Import SummarizedExperiment to avoid warnings

1.1.1

• Add batch effects to Splat simulation
• Make Splat group assignment probabilistic
• Update SplatParams with new parameters

1.1.0

• Bioconductor 3.6 devel

1.0.3

• Update citation

1.0.2

• Fix error handling when fitting means

1.0.1

• Fix scales in some difference plots
• Fix colours in difference plots
• Fix panel legends

1.0.0

• Bioconductor 3.5 release

0.99.15

• Add summariseDiff function
• Add BPPARAM argument to scDDSimulate
• Adjust default Splat DE factor parameters
• Add limits to zeros diff plots
• Remove estimation of dropout.present

0.99.14

• Add functions for making comparison panels
• Add panel section to vignette
• Change variance plot scale (for consistency)

0.99.13

• Modify how Lun2Params stores gene paramters to use data.frame
• Move sampling of genes/cells to lun2Simulate
• Return to old Lun2 nGenes estimate

0.99.12

• Add diffSCESets function
• Update compareSCESets plots
• Modify Lun2 nGenes estimate
• Modify how addFeatureStats names columns
• Add infinte bcv.df warning to splatSimulate

0.99.11

• Add parallel option to lun2Estimate
• Allow non-integer library sizes in Lun2Params
• Adjust dropout eta value
• Adjust comparison plots

0.99.10

• Improve Splat estimation procedure
• Update default Splat parameters
• Remove out.loProb Splat parameter
• Add MeanZeros plot to compareSCESets