NEWS.md

Version 1.1.8 (2017-10-13)

• Add BASiCS simulation
• Update Splatter citation
• Update Lun2 reference

Version 1.1.7 (2017-10-05)

• Add PhenoPath simulation
• Add ZINB-WaVE simulation
• Adjust mfaSimulate output

Version 1.1.6 (2017-10-02)

• Update scDD version
• Add mfa simulation

Version 1.1.5 (2017-09-13)

• Convert to SingleCellExperiment

Version 1.1.4 (2017-08-04)

• Fix group factors bug

Version 1.1.3 (2017-07-20)

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

Version 1.1.2 (2017-07-16)

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

Version 1.1.1 (2017-07-07)

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

Version 1.1.0 (2017-07-07)

• Bioconductor 3.6 devel

Version 1.0.3 (2017-05-26)

• Update citation

Version 1.0.2 (2017-05-15)

• Fix error handling when fitting means

Version 1.0.1 (2017-04-28)

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

Version 1.0.0 (2017-04-28)

• Bioconductor 3.5 release

Version 0.99.15 (2017-04-14)

• 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

Version 0.99.14 (2017-03-28)

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

Version 0.99.13 (2017-03-25)

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

Version 0.99.12 (2017-03-22)

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

Version 0.99.11 (2017-03-20)

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

Version 0.99.10 (2017-03-07)

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

Version 0.99.9 (2017-02-02)

• Add addGeneLengths function
• Update scDD reference

Version 0.99.8 (2017-01-23)

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

Version 0.99.7 (2017-01-10)

• Small changes to avoid NOTEs and reduce check time

Version 0.99.6 (2016-12-29)

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

Version 0.99.5 (2016-12-28)

• Set R_TESTS environment

Version 0.99.4 (2016-12-23)

• Version bump to start build

Version 0.99.3 (2016-12-21)

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

Version 0.99.2 (2016-12-13)

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

Version 0.99.1 (2016-12-12)

• Address Biocondutor build warnings, notes

Version 0.99.0 (2016-12-05)

• Submit to Bioconductor

Version 0.12.1 (2016-11-25)

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

Version 0.12.0 (2016-10-25)

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

Version 0.11.1 (2016-11-23)

• Fix bug in splatSimulatePaths that caused NAs

Version 0.11.0 (2016-11-22)

• Make compatible with Bioconductor 3.4

Version 0.10.1 (2016-10-17)

• Fix error for SCESets in lun2Estimate, scDDEstimate

Version 0.10.0 (2016-10-16)

• Add listSims function
• Add vignette

Version 0.9.0 (2016-10-15)

• Add scDD simulation

Version 0.8.0 (2016-10-15)

• Add Lun2 simulation

Version 0.7.0 (2016-10-14)

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

Version 0.6.0 (2016-10-12)

• Add Lun simulation
• Modify splatParams to take Lun parameters

Version 0.5.0 (2016-10-12)

• Add simple simulation

Version 0.4.0 (2016-10-12)

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

Version 0.3.0 (2016-10-06)

• Added parameter estimation functions

Version 0.2.0 (2016-10-06)

• Added splatParams object
• Added functions for interacting with splatParams