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digitalDLSorteR 0.1.0 (2021-10-08)

• Added a NEWS.md file to track changes to the package.

digitalDLSorteR 0.1.1 (2021-10-18)

• Added Solaris OS as one of the options in switch function (BiocParallel environment in estimateZinbwaveParams function).
• Some changes related to information about the package: messages during execution, README.

digitalDLSorteR 0.2.0 (2022-01-10)

• Implemented different ways to generate pseudo-bulk samples: MeanCPM, AddCPM, and AddRawCount (simBulkProfiles function).
• Implemented different ways to scale data before training: standarization and rescaling (trainDigitalDLSorterModel function).
• Vignettes updated.

digitalDLSorteR 0.3.0 (2022-05-24)

• The splatter dependency has been removed: instead of using splatter as a wrapper, zinbFit from the zinbwave package is used directly via the .zinbWaveModel function + the ZinbParametersModel class. This change affects some functions in terms of classes/objects. Previous pre-trained models (digitalDLSorteRmodels package) may not work properly. They will be generated soon.
• The edgeR dependency has been removed: CPM-related calculations have been implemented (.cpmCalculate function). Now, results may be slightly different from those obtained with edgeR.

digitalDLSorteR 0.3.1 (2022-10-04)

• The Matrix.utils dependency has been removed: instead of using the aggregate.Matrix function, it is used functions implemented in the base package.

digitalDLSorteR 0.3.2 (2022-11-10)

• Changed the way dense matrices (matrix) and data.frame objects are transformed into dgCMatrix objects.

digitalDLSorteR 1.0.1 (2024-02-05)

• Some name functions have been changed: createDDLSobject and trainDDLSModel.
• Loading data (createDDLSobject) has been changed: now, only 2,000 genes are used for deconvolution and bulk RNA-seq must be provided at the beginning of the workflow (see documentation).
• Fixed bugs: standardization of features before training.
• Vignette modified according to the new functions.
• HDF5Array update: use.for parameter has been deleted.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.