NEWS.md

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

DEVELOPMENT VERSION

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 \dontrun 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)

• New initialize method for Params objects (Fixes #132, PR #134 @wenjie2wang)

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

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.