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  • Luke Zappia's avatar
    b62f8ec3
    Merge branch 'batches' · b62f8ec3
    Luke Zappia authored
    * batches:
      Run checks
      Add batch effects to vignette
      Update splatEstimate to set batchCells
      Add batch effects to splatSimulate
      Update SplatParams
    b62f8ec3
    History
    Merge branch 'batches'
    Luke Zappia authored
    * batches:
      Run checks
      Add batch effects to vignette
      Update splatEstimate to set batchCells
      Add batch effects to splatSimulate
      Update SplatParams
To find the state of this project's repository at the time of any of these versions, check out the tags.

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