NEWS

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zinbwave 1.11.6 (2020-07-18)

• Fixed a bug in the initialization of beta_j.
• Fixed a bug in zinbsurf.
• Changed zinbwave default to 'K=2'.
• Fix bug in the initialization of W.

zinbwave 1.7.5 (2019-10-08)

• Changed default of 'zinbwave' to 'observationalWeights=FALSE' to speed up computations when weights are not needed.
• Added argument 'zeroinflation = TRUE': when set to FALSE a negative binomial model is fit.
• Removed dependence on the 'copula' package to avoid depending on 'gsl'.

zinbwave 1.5.3 (2019-04-19)

• Updated vignette to reflect new way of interacting with Seurat.
• Illustrate the use of approximate 'zinbsurf' function.

zinbwave 1.4.2 (2019-03-11)

• Fix bug in computeObservationalWeights.

zinbwave 1.3.1 (2018-05-09)

• New 'zinbsurf' function implements approximate method for large matrices.
• New option 'which_genes' in 'zinbwave' to specify which genes to use to compute 'W'.

zinbwave 1.1.6 (2018-04-17)

• 'zinbwave' now uses 'counts' assay by default.
• Users can now specify which assay to use to fit the zinb model.

zinbwave 1.1.5 (2018-02-15)

• Computational weights are computed in 'zinbwave' as saved as assay.
• Modified vignette to include example of Differential Expression.
• Improved documentation for 'zinbwave'.

zinbwave 0.99.10 (2017-10-23)

• Added AIC and BIC to decide number of factors
• Added function to compute observational weights for DE

zinbwave 0.99.7 (2017-07-17)

• 'zinbwave()' now returns a 'SingleCellExperiment' object.

zinbwave 0.99.6 (2017-07-05)

• Fixed bug in zinb.loglik.matrix to avoid Inf values

zinbwave 0.99.5 (2017-07-03)

• Added function computeDevianceResiduals() to compute residuals
• Added function imputeZeros() to use the model to impute technical zeros
• Added function zinbwave() to perform dimensionality reduction
• Changed vignette to illustrate new functions

zinbwave 0.99.4 (2017-06-08)

• Switch from parallel to BiocParallel
• Improvements to code efficiency, e.g., avoid copying ZinbModel objects

zinbwave 0.99.3 (2017-05-31)

• More informative Description: field
• Improved documentation
• Added getAlpha, getBeta, and getGamma accessor functions
• Improved show() method
• Vectorized code in zinbSim()
• Fixed bug that introduced an error when initializing an object with empty X or V
• Added tests on numerical correctness

zinbwave 0.99.2 (2017-05-12)

• New formula interface for SummarizedExperiment
• Add t-SNE example to vignette

zinbwave 0.99.0 (2017-05-09)

• Bumped version for submission to Bioconductor
• Minor changes to compile vignette
• Required R version 3.4

zinbwave 0.1.4 (2017-04-10)

• Improved documentation
• zinbSim now produces matrix of J x n dimension
• Removed unnecessary dependency on clusterExperiment
• Additional tests
• Better default for epsilon

zinbwave 0.1.2 (2017-03-29)

• New vignette
• Change name to zinbwave

zinbwave 0.1.0 (2016-09-23)

• Introducing S4 class zinbModel
• Major restructuring of the initialization and optimization (see vignette)
• Method zinbFit to fit a model
• Many other methods, including zinbInitialize, zinbOptimize, zinbSim