Skip to contents

Changelog

Source: NEWS.md

Version 1.32.0 (2025-04-16)

Bioconductor 3.21 release

Version 1.31.1 (2025-04-10)

  • Update NEWS for release

Version 1.31.0 (2024-10-30)

Bioconductor 3.21 devel

Version 1.30.0 (2024-10-30)

Bioconductor 3.20 release

Version 1.29.1 (2024-10-17)

  • Update roxygen2 version
  • Remove old CI config files
  • Add PR commands GitHub action
  • Re-configure pkgdown site
  • Add dependabot GitHub action
  • Update README

Version 1.29.0 (2024-05-01)

Bioconductor 3.20 devel

Version 1.28.0 (2024-05-01)

Bioconductor 3.19 release

Version 1.27.2 (2024-04-23)

  • Set for addGeneLengths to avoid depending on annotation packages
  • Update NEWS for Bioconductor 3.19 release

Version 1.27.1 (2024-03-26)

  • 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

Version 1.27.0 (2023-10-25)

Bioconductor 3.19 devel

Version 1.26.0 (2023-10-25)

Bioconductor 3.18 release

Version 1.25.1 (2023-10-11)

  • 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.

Version 1.25.0 (2023-04-26)

Bioconductor 3.18 devel

Version 1.24.0 (2023-04-26)

Bioconductor 3.17 release

Version 1.23.4 (2023-04-12)

  • Replace uses of ggplot2::aes_string() with ggplot2::aes() (Fixes #75)

Version 1.23.3 (2023-04-10)

  • Fix typo in DESCRIPTION

Version 1.23.2 (2023-04-05)

  • 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

Version 1.23.1 (2023-01-30)

  • Fix bug in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)

Version 1.23.0 (2022-11-02)

Bioconductor 3.17 devel

Version 1.22.0 (2022-11-02)

Bioconductor 3.16 release

Version 1.22.1 (2023-01-30)

  • Fix bug in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)

Version 1.22.0 (2022-11-02)

Bioconductor 3.16 release

Version 1.21.2 (2022-10-26)

  • 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

Version 1.21.1 (2022-08-11)

  • Fix bug in BASiCSSimulate() when spike.means is resampled (Fixes #153)

Version 1.21.0 (2022-04-27)

Bioconductor 3.16 devel

Version 1.20.0 (2022-04-27)

Bioconductor 3.15 release

Version 1.19.5 (2022-04-23)

  • Add starting point for dropout fit estimation (Fixes #142)
    • Idea borrowed from the modified splat implementation in the InferCNV package

Version 1.19.4 (2022-03-11)

Version 1.19.3 (2022-01-28)

  • Removed duplicated code in splatSimPathCellMeans() (Fixes #131)
  • Add additional fallback method for fitting dropout in splatEstimate() (Fixes #133)

Version 1.19.2 (2022-01-10)

  • 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)

Version 1.19.1 (2021-11-02)

  • Fixed bug where conditional eQTL effects were being incorrectly allocated in splatPop (Fixes #125, @azodichr)

Version 1.19.0 (2021-10-27)

Bioconductor 3.15 devel

Version 1.18.0 (2021-10-27)

Bioconductor 3.14 release

Version 1.18.1 (2021-11-02)

  • Fixed bug where conditional eQTL effects were being incorrectly allocated in splatPop (Fixes #125, @azodichr)

Version 1.18.2 (2022-01-10)

  • 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)

Version 1.17.3 (2021-10-07)

  • Improved checks for group.prob in SplatParams (Fixes #107)
  • Automatically rescale group.prob during setting if it doesn’t sum to 1

Version 1.17.2 (2021-10-06)

  • 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

Version 1.17.1 (2021-05-20)

  • Fix bug in validating splatPopParams

Version 1.17.0 (2021-05-20)

Bioconductor 3.14 devel

Version 1.16.0 (2021-05-20)

Bioconductor 3.13 release

Version 1.16.1 (2021-05-20)

  • Fix bug in validating splatPopParams

Version 1.15.3 (2021-05-18)

  • Modify sparsifyMatrices() to handle logical matrices
  • Adjust checking that vectors sum to 1 (Fixes #107)
  • Update NEWS.Rd for release

Version 1.15.2 (2021-05-11)

  • Updates to splatPop including conditional effects, multiplexed batch structure, and nCells per individual sampling. (PR #113)

Version 1.15.1 (2020-12-01)

  • Replace akima::aspline() with stats::spline(…, method = “natural”) in buildBridges() (Fixes #108)

Version 1.15.0 (2020-10-28)

Bioconductor 3.13 devel

Version 1.14.0 (2020-10-28)

Bioconductor 3.12 release

Version 1.14.1 (2020-12-01)

  • Replace akima::aspline() with stats::spline(…, method = “natural”) in buildBridges() (Fixes #108)

Version 1.13.2 (2020-10-25)

  • 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()

Version 1.13.1 (2020-10-22)

  • Add the splatPop simulation (PR #106)

Version 1.13.0 (2020-04-29)

  • Bioconductor 3.12 devel

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