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NEWS.md
file to track changes to the package.switch
function (BiocParallel environment in estimateZinbwaveParams
function).simBulkProfiles
function).trainDigitalDLSorterModel
function).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.edgeR
dependency has been removed: CPM-related calculations have been implemented (.cpmCalculate
function). Now, results may be slightly different from those obtained with edgeR
.Matrix.utils
dependency has been removed: instead of using the aggregate.Matrix
function, it is used functions implemented in the base
package.matrix
) and data.frame
objects are transformed into dgCMatrix
objects.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.
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