NEWS.md

In digitalDLSorteR: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

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 documentation built on Oct. 5, 2022, 9:05 a.m.