Merge branch 'master' into ci
* master: (49 commits) Fix where simpleSimulate stores params Check for counts assay when estimating from SCE Check spelling Build pkgdown Run checks Rename Splotch to Kersplat Add Splotch to listSims Document Splotch estimation functions Document Splotch simulation functions Minor Splotch changes Add doublets to SplotchSimulate Add ambient expression and empty cells to Splotch Rescale Phi when sampling in BASiCSSimulate Adjust BASiCSSimulate to match devel BASiCS Fix bug in NAMESPACE Add BCV adjustment to Splotch Add density sampling option for means, lib sizes Add violins to comparison plots Replace library size log-norm with density Fix splotchEstimate example ...
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- .Rbuildignore 2 additions, 0 deletions.Rbuildignore
- .gitignore 2 additions, 0 deletions.gitignore
- DESCRIPTION 13 additions, 10 deletionsDESCRIPTION
- NAMESPACE 24 additions, 0 deletionsNAMESPACE
- NEWS.md 166 additions, 5 deletionsNEWS.md
- R/AllClasses.R 177 additions, 14 deletionsR/AllClasses.R
- R/AllGenerics.R 43 additions, 10 deletionsR/AllGenerics.R
- R/BASiCS-estimate.R 7 additions, 6 deletionsR/BASiCS-estimate.R
- R/BASiCS-simulate.R 36 additions, 24 deletionsR/BASiCS-simulate.R
- R/KersplatParams-methods.R 305 additions, 0 deletionsR/KersplatParams-methods.R
- R/Params-methods.R 23 additions, 2 deletionsR/Params-methods.R
- R/SCE-functions.R 22 additions, 0 deletionsR/SCE-functions.R
- R/SimpleParams-methods.R 2 additions, 1 deletionR/SimpleParams-methods.R
- R/SplatParams-methods.R 26 additions, 5 deletionsR/SplatParams-methods.R
- R/ZINBParams-methods.R 7 additions, 6 deletionsR/ZINBParams-methods.R
- R/compare.R 300 additions, 195 deletionsR/compare.R
- R/kersplat-estimate.R 347 additions, 0 deletionsR/kersplat-estimate.R
- R/kersplat-simulate.R 936 additions, 0 deletionsR/kersplat-simulate.R
- R/listSims.R 5 additions, 0 deletionsR/listSims.R
- R/lun-estimate.R 4 additions, 3 deletionsR/lun-estimate.R
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