Bioconductor 3.20 devel
Bioconductor 3.19 release
- Set \dontrun for addGeneLengths to avoid depending on annotation packages
- Update NEWS for Bioconductor 3.19 release
- Properly prevent output from BASiCSEstimate() and scDDSimulate() when verbose = FALSE
- Minor adjustments to tests
- Set verbose = FALSE where needed
- Specify expected warnings
- Minor updates to documentation
- Replace package man page with auto-generated page
- Add GitHub usernames and Bioconductor URL to DESCRIPTION
- Add @keywords internal and @noRd to functions docs where needed
- Restyle code using styler
- Other minor fixes suggested by BiocCheck
Bioconductor 3.19 devel
Bioconductor 3.18 release
- Fix a bug in splatSimPathDE() where DE factors were not adjusted based on the path origin (path.from parameter). This affected paths where the path origin was not the simulation origin (path.from != 0), particularly when the path DE was minimal.
Bioconductor 3.18 devel
Bioconductor 3.17 release
- Replace uses of ggplot2::aes_string() with ggplot2::aes() (Fixes #75)
- Fix typo in DESCRIPTION
- Replace set.seed() with withr::with_seed()
- Switch scater and scuttle dependencies. scater is now suggested which saves a few dependencies
- Move ggplot2 to suggested for the same reason
- Fix bug in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)
Bioconductor 3.17 devel
Bioconductor 3.16 release
- Fix bug in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)
Bioconductor 3.16 release
- Fix a bug with non-matching rownames in splatPopSimulate() (PR #151 @azodichr, fixes #149)
- Fix a bug in splatPopSimulate() when batch.size is greater than the number of samples (PR #151 @azodichr)
- Additional splatPopSimulate tests
- Fix bug in BASiCSSimulate() when spike.means is resampled (Fixes #153)
Bioconductor 3.16 devel
Bioconductor 3.15 release
- Add starting point for dropout fit estimation (Fixes #142)
- Idea borrowed from the modified splat implementation in the InferCNV package
- New initialize method for Params objects (Fixes #132, PR #134 @wenjie2wang)
- Removed duplicated code in splatSimPathCellMeans() (Fixes #131)
- Add additional fallback method for fitting dropout in splatEstimate() (Fixes #133)
- Update the citation for the splatPop model (Fixes #128, PR #129 @azodichr)
- Update preprint DOIs for other models in listSims()
- Replace scran::computeSumFactors() with scuttle::pooledSizeFactors() in lun2Estimate() (Fixes #130)
- Fixed bug where conditional eQTL effects were being incorrectly allocated in splatPop (Fixes #125, @azodichr)
Bioconductor 3.15 devel
Bioconductor 3.14 release
- Fixed bug where conditional eQTL effects were being incorrectly allocated in splatPop (Fixes #125, @azodichr)
- Update the citation for the splatPop model (Fixes #128, PR #129 @azodichr)
- Update preprint DOIs for other models in listSims()
- Replace scran::computeSumFactors() with scuttle::pooledSizeFactors() in lun2Estimate() (Fixes #130)
- Improved checks for group.prob in SplatParams (Fixes #107)
- Automatically rescale group.prob during setting if it doesn't sum to 1
- Fixed duplicate cell names in splatPopSimulate (Fixes #118)
- Add functionality to simulate directly from empirical values to splatPop
- Add eqtl.coreg parameter to splatPop
- Fixed a bug where too many cells were simulated in splatPop with multiple batches
- Fix bug in validating splatPopParams
Bioconductor 3.14 devel
Bioconductor 3.13 release
- Fix bug in validating splatPopParams
- Modify sparsifyMatrices() to handle logical matrices
- Adjust checking that vectors sum to 1 (Fixes #107)
- Update NEWS.Rd for release
- Updates to splatPop including conditional effects, multiplexed batch structure, and nCells per individual sampling. (PR #113)
- Replace akima::aspline() with stats::spline(..., method = "natural") in buildBridges() (Fixes #108)
Bioconductor 3.13 devel
Bioconductor 3.12 release
- Replace akima::aspline() with stats::spline(..., method = "natural") in buildBridges() (Fixes #108)
- Add batch.rmEffect parameter to SplatParams (PR #103)
- Add minimiseSCE() function
- Automatically sparsify assays by default in all simulations
- Add checkDependencies() function
- Replace DropletUtils::downsampleMatrix() with scuttle::downsampleMatrix()
- Add the splatPop simulation (PR #106)
- Bioconductor 3.12 devel
- Bioconductor 3.11 release
- Fix warning about typo in NEWS.Rd
- Fix note about partial argument matching
- Use alternative algorithm if splatEstimate dropout fitting fails (Fixes #96 and #31)
- Adjust paths example in vignette (Fixes #90)
- Use option for Kersplat warning to avoid NOTE about ':::'
- Check for cycles in path.from (Fixes #91)
- Update tests to work with checkmate 2.0.0
- Add suggested checks to Kersplat tests and examples
- Update tests to work with checkmate 2.0.0
- Replace defunct scater function in vignettes
- Update Roxygen version
- Bioconductor 3.11 devel
- Bioconductor 3.10 release
- Update NEWS.Rd
- Update scater QC function names
- Add missing documentation for sce argument in getCounts
- Update maintainer email address
- 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)
- Run checks
- Document Splotch estimation functions
- Add Splotch to listSims
- Rename Splotch to Kersplat
- Document Splotch simulation functions
- 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
- Add doublets to splotchSimulate
- Add ambient expression and empty cells to splotchSimulate
- Merge master into splotch branch
- Rescale when sampling Phi in BASiCSSimulate
- Adjust BASiCSSimulate to match development version of BASiCS
- Merge master into splotch branch
- Fix bug in NAMESPACE
- Add BCV adjustment to Splotch simulation
- Use new exponential correction for bcv.common
- Add density sampling options for means and library sizes
- Replace library size log-normal with density and rejection sampling
- Add violins to comparison plots
- Merge master into splotch branch
- Fix dataset in splotchEstimate example
- 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
- Add expression outliers to Splotch
- Fix bug in selectFit
- Add splotchEstimate function
- Simulate counts in splotchSimulate
- Split splotchSimulate into separate functions for each stage
- Merge master into splotch branch
- Remove deprecated scater functions
- Topologically sort Splotch paths
- Add library size parameters to SplotchParams
- Simulate cell means in splotchSimulate
- Add paths parameters to SplotchParams
- Add mean parameters to SplotchParams
- Add SplotchParams object
- Add variable gene correlation plot to compareSCEs
- 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
- Bioconductor 3.10 devel
- Bioconductor 3.9 release
- Add Splat parameters vignette
- Fix spelling
- Allow SplatParams parameters to be set in any order
- Minor changes to documentation
- Protect against integer overflow in simulation functions
- Fix order of groups in splatSimulate
- Add ImmunoOncology biocViews tag at request of Bioconductor team
- Fix bugs in vignette
- Bioconductor 3.9 devel
- Add ImmunoOncology biocViews tag at request of Bioconductor team
- Bioconductor 3.8 release
- Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()
- Fix BASiCSEstimate tests
- Fix installation instructions
- Fix bug in BASiCSEstimate when no spike-ins provided
- Add missing regression argument to BASiCSEstimate
- Add new BASiCS tests
- 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
- Fix normality testing error in splatEstLib
- Correct p-value cutoff in normality test
- Sample library sizes for normality testing if > 5000 cells
- Bioconductor 3.7 devel
- Fix bug in BASiCSEstimate when no spike-ins provided
- Add missing regression argument to BASiCSEstimate
- Add new BASiCS tests
- Fix normality testing error in splatEstLib
- Correct p-value cutoff in normality test
- Sample library sizes for normality testing if > 5000 cells
- Bioconductor 3.7 release
- Set seed in sparseDCEstimate tests
- Replace dropout.present with dropout.type in SplatParams
- Allows users to set dropout by experiment, batch, group or cell
- 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
- Add option to use a normal distribution for library sizes in Splat simulations
- Replace dropout.present with dropout.type in SplatParams
- Allows more control over dropout.mid and dropout.shape
- Fix parameter passing bug in scDDEstimate
- 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
- Fix error in vignette caused by changes in scater
- Bioconductor 3.7 devel
- Fix parameter passing bug in scDDEstimate
- Fix zinbwave installation error
- Bioconductor 3.6 release
- Add BASiCS simulation
- Update Splatter citation
- Update Lun2 reference
- Add PhenoPath simulation
- Add ZINB-WaVE simulation
- Adjust mfaSimulate output
- Update scDD version
- Add mfa simulation
- Convert to SingleCellExperiment
- Fix group factors bug
- Add verbose option to scDDEstimate
- Change "mean-dropout" to "mean-zeros" in compareSCESets
- Update summariseDiff
- Update scDDEstimate, now estimates gene types
- Fix error in lun2Estimate
- Import SummarizedExperiment to avoid warnings
- Add batch effects to Splat simulation
- Make Splat group assignment probabilistic
- Update SplatParams with new parameters
- Bioconductor 3.6 devel
- Update citation
- Fix error handling when fitting means
- Fix scales in some difference plots
- Fix colours in difference plots
- Fix panel legends
- Bioconductor 3.5 release
- 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
- Add functions for making comparison panels
- Add panel section to vignette
- Change variance plot scale (for consistency)
- Modify how Lun2Params stores gene parameters to use data.frame
- Move sampling of genes/cells to lun2Simulate
- Return to old Lun2 nGenes estimate
- Add diffSCESets function
- Update compareSCESets plots
- Modify Lun2 nGenes estimate
- Modify how addFeatureStats names columns
- Add infinite bcv.df warning to splatSimulate
- Add parallel option to lun2Estimate
- Allow non-integer library sizes in Lun2Params
- Adjust dropout eta value
- Adjust comparison plots
- Improve Splat estimation procedure
- Update default Splat parameters
- Remove out.loProb Splat parameter
- Add MeanZeros plot to compareSCESets
- Add addGeneLengths function
- Update scDD reference
- Fix bug that meant non-linear path factors weren't stored in output
- Small changes to avoid NOTEs and reduce check time
- Add installation to vignette
- Add detail about counts matrix to vignette
- Replace 1:x with seq_len/seq_along
- Set R_TESTS environment
- Version bump to start build
- Fix to match Bioconductor version of scDD
- Add logo to repository
- Add rownames, colnames to matrices in splatSimulate, lunSimulate
- Bump R version to 3.4
- Address Biocondutor build warnings, notes
- Submit to Bioconductor
- Fix bug in compareSCESets
- Dataset order is now kept in plots
- Add compareSCESets function
- Update vignette
- Fix LunParams validity bug
- Add logo
- Fix bug in splatSimulatePaths that caused NAs
- Make compatible with Bioconductor 3.4
- Fix error for SCESets in lun2Estimate, scDDEstimate
- Add listSims function
- Add vignette
- Add scDD simulation
- Add Lun2 simulation
- Redesign how parameters are stored
- Each simulation now has it's own S4 Params class
- Modify existing simulations to use new parameter objects
- Add Lun simulation
- Modify splatParams to take Lun parameters
- Add simple simulation
- Add splatter simulations
- Modify some parts of splatParams and fix bugs
- Added parameter estimation functions
- Added splatParams object
- Added functions for interacting with splatParams