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All releases
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
Contents
1.1.5
1.1.4
1.1.3
1.1.2
1.1.1
1.1.0
1.0.3
1.0.2
1.0.1
1.0.0
0.99.0