The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class.
This class is initialized from a matrix of expression values Methods that operate on CellDataSet objects constitute the basic Monocle workflow.
Matrix of class numeric, containing the source values computed by Independent Components Analysis.
Matrix of class numeric, containing the whitened expression values computed during Independent Components Analysis.
Matrix of class numeric, containing the weight values computed by Independent Components Analysis.
A Matrix of class numeric, containing the pre-whitening matrix computed by Independent Components Analysis.
An Object of class igraph, containing the minimum spanning tree used by Monocle to order cells according to progress through a biological process.
A Matrix of class numeric, containing the pairwise distances between cells in the reduced dimension space.
An Object of class vglmff, specifying the VGAM family function used for expression responses.
A numeric value specifying the minimum expression level considered to be true expression.
An environment containing lists, one for each set of estimated dispersion values. See estimateDispersions.
A string encoding how this CellDataSet has been reduced in dimensionality
An environment of auxilliary data structures used by various steps in Monocle. Not to be accessed by users directly.
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