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.