Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of splatter

splatter - Bioconductor 3.21

No changes to report

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.30.0...v1.32.0

- R
Published by lazappi 11 months ago

splatter - Bioconductor 3.20

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

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.28.0...v1.30.0

- R
Published by lazappi over 1 year ago

splatter - Bioconductor 3.19

  • Properly prevent output from BASiCSEstimate() and scDDSimulate() when verbose = FALSE
  • Minor adjustments to tests to set verbose = FALSE and specify expected warnings
  • Replace the package man page with an auto-generated page
  • Add GitHub usernames and the Bioconductor package URL to DESCRIPTION
  • Add @keywords internal and @noRd to function docs where needed
  • Modernise code by restyling using styler and fix other minor issues suggested by BiocCheck()

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.26.0...v1.28.0

- R
Published by lazappi almost 2 years ago

splatter - Bioconductor 3.18

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.

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.24.0...v1.26.0

- R
Published by lazappi over 2 years ago

splatter - Bioconductor 3.17

  • Fixed bugs in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)
  • Replace all uses of set.seed with withr::with_seed() (@lazappi)
  • Reduced core dependencies by importing scuttle rather than scater (scater is suggested) and making ggplot2 a suggested dependency (@lazappi , fixes #75)

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.22.0...v1.24.0

- R
Published by lazappi almost 3 years ago

splatter - Bioconductor 3.16

  • Fixed a bug in BASiCSSimulate() when spike.means is resampled (Fixes #153)
  • Fixed bugs in splatPopSimulate() with non-matching rownames and when sampling batches (PR #151 @azodichr, fixes #149)

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.20.0...v1.22.0

- R
Published by lazappi over 3 years ago

splatter - Bioconductor 3.15

  • The splatPop simulation is now published in Genome Biology 🎉 ! (Fixes #128, PR #129 @azodichr)
  • Improved initialisation of Params objects (Fixes #132, PR #134 @wenjie2wang)
  • Improved fitting of dropout in splatEstimate()
    • Better initialisation of fitting as suggested by the InferCNV package (Fixes #142)
    • Additional fallback method (Fixes #133)
  • Bug fixes for the splat simulation
    • Replace scran::computeSumFactors() with scuttle::pooledSizeFactors() in lun2Estimate() (Fixes #130)
    • Removed duplicated code in splatSimPathCellMeans() (Fixes #131)
  • Bug fixes for the the splatPop simulation
    • * Fixed bug where conditional eQTL effects were being incorrectly allocated (Fixes #125, @azodichr)

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.18.0...v1.20.0

- R
Published by lazappi almost 4 years ago

splatter - Bioconductor 3.14

  • Updates to the splatPop simulation (from @azodichr)
    • 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 (#118)
  • Improved checks for group.prob in SplatParams (#107)
    • Automatically rescale group.prob during setting if it doesn't sum to 1

Full Changelog: https://github.com/Oshlack/splatter/compare/v1.16.0...v1.18.0

- R
Published by lazappi over 4 years ago

splatter - Bioconductor 3.13

  • Substantial updates to the splatPop simulation (from @azodichr)
    • 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
  • Logical matrices should now be handled correctly when minimising output SingleCellExperiment objects
  • Other minor fixes

- R
Published by lazappi almost 5 years ago

splatter - Bioconductor 3.12

  • Add the splatPop simulation. This is a extension to the splat simulation contributed by @azodichr and @davismcc that adds population effects. It allows you to specify relatedness between individuals and generate cell-type specific eQTL effects. (PR #106)
  • Add a batch.rmEffect parameter to the Splat simulation. This allows generation of a paired simulation without any batch effects. (From @daynefiler PR #103)
  • Add a new minimiseSCE() function which can be used to remove unneeded information from simulation output (or any SingleCellExperiment).
  • 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.
  • Users will now be automatically prompted to install packages if they try to use a simulation for which the suggested dependencies are not available.

- R
Published by lazappi over 5 years ago

splatter - Bioconductor 3.11

  • Add checks for cycles in the Splat path.from parameter.
  • Use alternative algorithm if fitting dropout fails in splatEstimate().
  • Adjust paths example in vignette.
  • Replace defunct functions in vignettes.
  • Minor fixes for compatibility with updates to other packages.

- R
Published by lazappi almost 6 years ago

splatter - Bioconductor 3.10

  • Add the (experimental) Kersplat simulation model. This model incorporates a gene network and other useful features.
  • Refactor the summariseDiff() function and add the KS statistic.
  • Add variable gene correlation plot to compareSCEs() and violins to other comparison plots.
  • Check for counts assay when estimating from SingleCellExperiment objects.
  • Fix where simpleSimulate() stores parameters.
  • 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 and add checks for suggested packages.
  • Various fixes for compatibility with updates to other packages.

- R
Published by lazappi about 6 years ago

splatter - Bioconductor 3.9 release

  • Add a Splat parameters vignette
  • Rename the Splat path.length parameter to path.nSteps
  • Fix a bug with parameter order in setParams
  • Fix a bug where Splat groups were being simulated in alphanumeric order
  • Protect against integer overflow in simulation functions

- R
Published by lazappi almost 7 years ago

splatter - Bioconductor 3.8 release

  • Fix bug and improve normality testing in splatEstLib
  • Fixes for compatibility with the latest version of BASiCS, BASiCSEstimate now uses the regression method
  • Fix bug in getLNormFactors when reversing factors less than one
  • Various updates to tests and documentation

- R
Published by lazappi over 7 years ago

splatter - Bioconductor 3.7 release

  • Move scater to Imports and add scater version
  • Remove lingering references to SCESets
  • Add option to use a normal distribution for library sizes in Splat simulations
  • Allow Splat dropout parameters to be specified by experiment, batch, group or cell
  • Add SparseDC simulation
  • Rename params in metadata slot of simulation to Params for consistency
  • Improve and colourise Params print output
  • Improve test coverage
  • Various other minor updates and bug fixes

- R
Published by lazappi almost 8 years ago

splatter - Version 1.2.0

Bioconductor 3.6 release version

- R
Published by lazappi over 8 years ago

splatter - Version 1.1.3 (BASiCS)

Version 1.1.3 of Splatter with the BASiCS simulation. This is the version of Splatter used in the response to reviewers for the Splatter paper https://doi.org/10.5281/zenodo.833572.

- R
Published by lazappi over 8 years ago