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

0.99.9

• Add addGeneLengths function
• Update scDD reference

0.99.8

• Fix bug that meant non-linear path factors weren't stored in output

0.99.7

• Small changes to avoid NOTEs and reduce check time

0.99.6

• Add installation to vignette
• Add detail about counts matrix to vignette
• Replace 1:x with seq_len/seq_along

0.99.5

• Set R_TESTS environment

0.99.4

• Version bump to start build

splatter 0.99.3

• Fix to match Bioconductor version of scDD
• Add logo to repository

splatter 0.99.2

• Add rownames, colnames to matrices in splatSimulate, lunSimulate
• Bump R version to 3.4

splatter 0.99.1

• Address Biocondutor build warnings, notes

splatter 0.99.0

• Submit to Bioconductor

splatter 0.12.1

• Fix bug in compareSCESets
• Dataset order is now kept in plots

splatter 0.12.0

• Add compareSCESets function
• Update vignette
• Fix LunParams validity bug
• Add logo

splatter 0.11.1

• Fix bug in splatSimulatePaths that caused NAs

splatter 0.11.0

• Make compatible with Bioconductor 3.4

splatter 0.10.1

• Fix error for SCESets in lun2Estimate, scDDEstimate

splatter 0.10.0

• Add listSims function
• Add vignette

splatter 0.9.0

• Add scDD simulation

splatter 0.8.0

• Add Lun2 simulation

splatter 0.7.0

• Redesign how parameters are stored
• Each simulation now has it's own S4 Params class
• Modify exisiting simulations to use new parameter objects

splatter 0.6.0

• Add Lun simulation
• Modify splatParams to take Lun parameters

splatter 0.5.0

• Add simple simulation

splatter 0.4.0

• Add splatter simulations
• Modify some parts of splatParams and fix bugs

splatter 0.3.0

• Added parameter estimation functions

splatter 0.2.0

• Added splatParams object
• Added functions for interacting with splatParams