Newer
Older
# 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
# 1.0.2
* Fix error handling when fitting means
# 1.0.1
* Fix scales in some difference plots
* Fix colours in difference plots
* Fix panel legends
# 0.99.15
* Add summariseDiff function
* Add BPPARAM argument to scDDSimulate
* 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
# 0.99.4
* 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 0.7.0
* 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