Changes in version 1.30.0 (2024-10-30)
o
Minor maintenance chores:
• Update roxygen2 version
• Remove old CI config files
• Add PR commands GitHub action
• Re-configure pkgdown site
• Add dependabot GitHub action
• Update README
Changes in version 1.28.0 (2024-05-01)
o
Properly prevent output from BASiCSEstimate() and
scDDSimulate() when verbose = FALSE
o
Minor adjustments to tests to set verbose = FALSE and specify
expected warnings
o
Replace the package man page with an auto-generated page
o
Add GitHub usernames and the Bioconductor package URL to
description
o
Add @keywords internal and @noRd to function docs where needed
o
Modernise code by restyling using styler and fix other minor
issues suggested by BiocCheck
Changes in version 1.26.0 (2023-10-25)
o
Fixed 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 (i.e. path.from != 0), particularly when the path DE
was minimal. With this fix paths should no longer drift
towards the origin.
Changes in version 1.24.0 (2023-04-26)
o
Fixed bugs in splatPopSimulate() where conditional group
assignments were incorrect when batch effects were applied
(from Christina Azodi)
o
Reduced core dependencies by importing scuttle rather than
scater (scater is suggested) and making ggplot2 a suggested
dependency.
Changes in version 1.22.0 (2022-10-31)
o
Fixed a bug in BASiSSimulate() when spike.means is resampled
o
Fixed bugs in splatPopSimulate() with non-matching rownames and
when sampling batches
Changes in version 1.20.0 (2022-04-27)
o
The splatPop simulation is now published
doi.org/10.1186/s13059-021-02546-1!
o Improved initalisation of Params objects (from Wenjie Wang)
o
Improved fitting of dropout in splatEstimate()
• Better initialisation of fitting as suggested by the
InferCNV package
• Additional fallback method
o Bug fixes for the splat simulation
o
Bug fixes for the the splatPop simulation (from Christina
Azodi)
Changes in version 1.18.0 (2021-10-27)
o
Updates to the splatPop simulation (from Christina Azodi)
• Added functionality to simulate directly from empirical
values
• Added eqtl.coreg parameter to splatPop
• Fixed a bug where too many cells were simulated in splatPop
with multiple batches
• Fixed duplicate cell names in splatPopSimulate
o
Improved checks for group.prob in SplatParams
o
Automatically rescale group.prob during setting if it doesn't
sum to 1
Changes in version 1.16.0 (2021-05-20)
o
Substantial updates to the splatPop simulation (from Christina
Azodi)
• Added ability to simulate data with complex multiplexed
sequencing designs
• Added simulation of “conditional†effects, where a subset
of DE and eQTL effects are applied to only a subset of
individuals (e.g. disease vs. healthy samples)
• Added the ability to simulate different numbers of cells
for each sample, sampled from a gamma distribution.
• Updates to the splatPop vignette describing these changes
o
Logical matrices should now be handled correctly when
minimising output SingleCellExperiment objects
o
Other minor fixes
Changes in version 1.14.0 (2020-10-28)
o Add the splatPop simulation. This is a extension to the splat
simulation contributed by Christina Azodi and Davis McCarthy
that adds population effects. It allows you to specify
relatedness between individuals and generate cell-type specific
eQTL effects.
o Add a batch.rmEffect parameter to the Splat simulation. This
allows generation of a paired simulation without any batch
effects.
o Add a new minimiseSCE function which can be used to remove
unneeded information from simulation output (or any
SingleCellExperiment)
o All simulations now return sparse assay matrices by default
when they would be smaller than the equivalent dense matrix.
This is controlled by a new sparsify argument.
o Users will now be automatically prompted to install packages if
they try to use a simulation for which the suggested
dependencies are not available
Changes in version 1.12.0 (2020-04-20)
o Add checks for cycles in the Splat path.from parameter.
o Use alternative algorithm if fitting dropout fails in
splatEstimate.
o Adjust paths example in vignette.
o Replace defunct functions in vignettes.
o Minor fixes for compatibility with updates to other packages.
Changes in version 1.10.0 (2019-10-20)
o Add the (experimental) Kersplat simulation model. This model
incorporates a gene network and other useful features.
o Refactor the summariseDiff function and add the KS statistic.
o Add variable gene correlation plot to compareSCEs and violins
to other comparison plots.
o Check for counts assay when estimating from
SingleCellExperiment objects.
o Fix where simpleSimulate stores parameters.
o Fix bugs where parameters were not being passed correctly in
BASiCSEstimate and sparseDCEstimate.
o Replace the sc_example_counts dataset from scater with the
mockSCE function.
o Tidy and improve estimation function examples and add checks
for suggested packages.
o Various fixes for compatibility with updates to other packages.
Changes in version 1.8.0 (2019-04-18)
o Add a Splat parameters vignette
o Rename the Splat path.length parameter to path.nSteps
o Fix a bug with parameter order in setParams
o Fix a bug where Splat groups were being simulated in
alphanumeric order
o Protect against integer overflow in simulation functions
Changes in version 1.6.0 (2018-10-29)
o Fix bug and improve normality testing in splatEstLib
o Fixes for compatibility with the latest version of BASiCS,
BASiCSEstimate now uses the regression method
o Fix bug in getLNormFactors when reversing factors less than one
o Various updates to tests and documentation
Changes in version 1.3.5 (2018-04-25)
o Move scater to Imports and add scater version
o Remove lingering references to SCESets
o Add option to use a normal distribution for library sizes in
Splat simulations
o Allow Splat dropout parameters to be specified by experiment,
batch, group or cell
o Add SparseDC simulation
o Rename params in metadata slot of simulation to Params for
consistency
o Improve and colourise Params print output
o Improve test coverage
o Various other minor updates and bug fixes
Changes in version 1.1.8 (2017-10-13)
o Now published in Genome Biology!
o Converted to the SingleCellExperiment object
o Added new simulations: BASiCS, mfa, PhenoPath, ZINB-WaVE
o Added batch effects to the Splat simulation. This required a
change to the SplatParams object.
o Improved scDD estimation
o Added and improved comparison functions
o Improved default Splat parameters and estimation
o Improvements to the Lun2Params object
o Added addGeneLength function
o Updated simulation references
o Various other minor updates and bug fixes
Changes in version 0.99.16 (2017-04-23)
o Splatter is a package for the simple simulation of single-cell
RNA-seq data, including:
o Multiple simulation models
o Parameter estimation from real data
o Functions for comparing simulations and real datasets
o Simulation of complex groups and differentiation paths
Changes in version 0.99.0 (2016-12-05)
o Package prepared for Bioconductor submission.