Toggle navigation
Splatter
1.13.0
Get started
Reference
Articles
Splat simulation parameters
Changelog
Changelog
Source:
NEWS.md
Version 1.12.0 (2020-04-29)
Bioconductor 3.11 release
Version 1.11.6 (2020-04-22)
Fix warning about typo in NEWS.Rd
Fix note about partial argument matching
Version 1.11.5 (2020-04-20)
Use alternative algorithm if splatEstimate dropout fitting fails (Fixes
#96
and
#31
)
Version 1.11.4 (2020-04-01)
Adjust paths example in vignette (Fixes
#90
)
Use option for Kersplat warning to avoid NOTE about ‘:::’
Version 1.11.3 (2020-02-20)
Check for cycles in path.from (Fixes
#91
)
Version 1.11.2 (2020-02-14)
Update tests to work with checkmate 2.0.0
Add suggested checks to Kersplat tests and examples
Version 1.10.1 (2020-02-14)
Update tests to work with checkmate 2.0.0
Version 1.11.1 (2010-01-30)
Replace defunct scater function in vignettes
Update Roxygen version
Version 1.11.0 (2019-10-30)
Bioconductor 3.11 devel
Version 1.10.0 (2019-10-30)
Bioconductor 3.10 release
Version 1.9.11 (2019-10-20)
Update NEWS.Rd
Version 1.9.10 (2019-10-20)
Update scater QC function names
Version 1.9.9 (2019-10-16)
Add missing documentation for sce argument in getCounts
Update maintainer email address
Version 1.9.8 (2019-10-11)
Add Kersplat simulation! Still experimental but is useable.
Check for counts assay when estimating from SingleCellExperiment objects (Fixes
#82
)
Fix where simpleSimulate stores parameters (Fixes
#72
)
Version 1.9.7.9019 (2019-10-11)
Run checks
Version 1.9.7.9018 (2019-10-10)
Document Splotch estimation functions
Add Splotch to listSims
Rename Splotch to Kersplat
Version 1.9.7.9017 (2019-10-09)
Document Splotch simulation functions
Version 1.9.7.9016 (2019-10-01)
Change the default SplotchParams cell design to place cells at end of path
Add one time warning for Splotch simulation
Avoid unnecessarily resetting cells.design in SplotchParams
Version 1.9.7.9015 (2019-09-26)
Add doublets to splotchSimulate
Version 1.9.7.9014 (2019-09-24)
Add ambient expression and empty cells to splotchSimulate
Version 1.9.7.9013 (2019-09-19)
Merge master into splotch branch
Version 1.9.7 (2019-09-19)
Rescale when sampling Phi in BASiCSSimulate
Version 1.9.6 (2019-09-17)
Adjust BASiCSSimulate to match development version of BASiCS
Version 1.9.5.9012 (2019-09-09)
Merge master into splotch branch
Version 1.9.5 (2019-09-09)
Fix bug in NAMESPACE
Version 1.9.4.9011 (2019-08-29)
Add BCV adjustment to Splotch simulation
Use new exponential correction for bcv.common
Version 1.9.4.9010 (2019-08-22)
Add density sampling options for means and library sizes
Version 1.9.4.9009 (2019-08-21)
Replace library size log-normal with density and rejection sampling
Add violins to comparison plots
Version 1.9.4.9008 (2019-08-20)
Merge master into splotch branch
Fix dataset in splotchEstimate example
Version 1.9.4 (2019-08-20)
Fix deprecated column name in diffSCEs QQ plots
Fix bugs where parameters were not being passed correctly in BASiCSEstimate and sparseDCEstimate
Replace the sc_example_counts dataset from scater with the mockSCE function
Tidy and improve estimation function examples
Version 1.9.3.9008 (2019-08-20)
Add expression outliers to Splotch
Version 1.9.3.9007 (2019-08-14)
Fix bug in selectFit
Version 1.9.3.9006 (2019-08-13)
Add splotchEstimate function
Version 1.9.3.9005 (2019-08-08)
Simulate counts in splotchSimulate
Split splotchSimulate into separate functions for each stage
Version 1.9.3.9004 (2019-08-08)
Merge master into splotch branch
Version 1.9.3 (2019-08-08)
Remove deprecated scater functions
Version 1.9.2.9003 (2019-07-17)
Topologically sort Splotch paths
Add library size parameters to SplotchParams
Simulate cell means in splotchSimulate
Version 1.9.2.9002 (2019-07-16)
Add paths parameters to SplotchParams
Version 1.9.2.9001 (2019-07-16)
Add mean parameters to SplotchParams
Version 1.9.2.9000 (2019-07-11)
Add SplotchParams object
Version 1.9.2 (2019-06-13)
Add variable gene correlation plot to compareSCEs
Version 1.9.1 (2019-06-05)
Refactor the summariseDiff function
Add the KS statistic to summariseDiff
Set gam method for fitted lines in comparison plots
Add checks for suggested packages in examples
Version 1.9.0 (2019-05-03)
Bioconductor 3.10 devel
Version 1.8.0 (2019-05-03)
Bioconductor 3.9 release
Version 1.7.5 (2018-04-18)
Add Splat parameters vignette
Fix spelling
Version 1.7.4 (2018-04-17)
Allow SplatParams parameters to be set in any order
Version 1.7.3 (2018-04-15)
Minor changes to documentation
Protect against integer overflow in simulation functions
Fix order of groups in splatSimulate
Version 1.7.2 (2018-12-06)
Add ImmunoOncology biocViews tag at request of Bioconductor team
Version 1.7.1 (2018-11-17)
Fix bugs in vignette
Version 1.7.0 (2018-11-01)
Bioconductor 3.9 devel
Version 1.6.1 (2018-12-06)
Add ImmunoOncology biocViews tag at request of Bioconductor team
Version 1.6.0 (2018-11-01)
Bioconductor 3.8 release
Version 1.5.8 (2018-10-22)
Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()
Version 1.5.7 (2018-10-03)
Fix BASiCSEstimate tests
Version 1.5.4 (2018-08-30)
Fix installation instructions
Version 1.5.3 (2018-08-20)
Fix bug in BASiCSEstimate when no spike-ins provided
Version 1.5.2.9000 (2018-08-16)
Add missing regression argument to BASiCSEstimate
Add new BASiCS tests
Version 1.5.2 (2018-08-16)
Fix bug in getLNormFactors when reversing factors less than one
Update documentation to new Roxygen version (6.1.0)
Change variable name in vignette for compatibility with scater
Add suggested package checks to tests
Version 1.5.1 (2018-06-12)
Fix normality testing error in splatEstLib
Correct p-value cutoff in normality test
Sample library sizes for normality testing if > 5000 cells
Version 1.5.0 (2018-05-02)
Bioconductor 3.7 devel
Version 1.4.3 (2018-08-20)
Fix bug in BASiCSEstimate when no spike-ins provided
Version 1.4.2 (2018-08-16)
Add missing regression argument to BASiCSEstimate
Add new BASiCS tests
Version 1.4.1 (2018-06-12)
Fix normality testing error in splatEstLib
Correct p-value cutoff in normality test
Sample library sizes for normality testing if > 5000 cells
Version 1.4.0 (2018-05-02)
Bioconductor 3.7 release
Version 1.3.6 (2018-04-30)
Set seed in sparseDCEstimate tests
Version 1.3.5 (2018-04-25)
Replace dropout.present with dropout.type in SplatParams
Allows users to set dropout by experiment, batch, group or cell
Version 1.3.4 (2018-04-19)
Add option to use a normal distribution for library sizes in Splat simulations
Add SparseDC simulation
Rename params in metadata slot of simulation to Params for consistency
Add checks to SplatParams to reset path.from if nGroups changes
Improve printing of parameters stored as data.frames
Colourise Params print output and listSims output
Improve warning message when fitting means in splatEstimate fails
Simplify problematic documentation links
Version 1.3.3.9010 (2018-04-12)
Add option to use a normal distribution for library sizes in Splat simulations
Version 1.3.3.9000 (2018-04-12)
Replace dropout.present with dropout.type in SplatParams
Allows more control over dropout.mid and dropout.shape
Version 1.3.3 (2018-03-27)
Fix parameter passing bug in scDDEstimate
Version 1.3.2 (2018-01-31)
Fix QC names that have been changed in scater
Move scater to Imports and add scater version
Remove lingering references to SCESets
Add more tests
Version 1.3.1 (2018-01-03)
Fix error in vignette caused by changes in scater
Version 1.3.0 (2017-10-13)
Bioconductor 3.7 devel
Version 1.2.2 (2018-03-27)
Fix parameter passing bug in scDDEstimate
Version 1.2.1 (2017-11-23)
Fix zinbwave installation error
Version 1.2.0 (2017-10-30)
Bioconductor 3.6 release
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 parameters 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 infinite 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 existing 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