CellDataSet             The CellDataSet class
cellPairwiseDistances   Retrieves a matrix capturing distances between
                        each cell in the reduced-dimensionality space
cellPairwiseDistances<-
                        Sets the matrix containing distances between
                        each pair of cells used by Monocle during cell
                        ordering. Not intended to be called directly.
clusterGenes            Plots the minimum spanning tree on cells.
compareModels           Compare model fits
detectGenes             Sets the global expression detection threshold
                        to be used with this CellDataSet. Counts how
                        many cells each feature in a CellDataSet object
                        that are detectably expressed above a minimum
                        threshold. Also counts the number of genes
                        above this threshold are detectable in each
                        cell.
differentialGeneTest    Tests each gene for differential expression as
                        a function of progress through a biological
                        process, or according to other covariates as
                        specified.
fitModel                Fits a model for each gene in a CellDataSet
                        object.
minSpanningTree         Retrieves the minimum spanning tree generated
                        by Monocle during cell ordering.
minSpanningTree<-       Sets the minimum spanning tree used by Monocle
                        during cell ordering. Not intended to be called
                        directly.
newCellDataSet          Creates a new CellDateSet object.
orderCells              Orders cells according to progress through a
                        learned biological process.
plot_clusters           Plots the minimum spanning tree on cells.
plot_genes_in_pseudotime
                        Plots expression for one or more genes as a
                        function of pseudotime
plot_genes_jitter       Plots expression for one or more genes as a
                        jittered, grouped points
plot_genes_positive_cells
                        Plots the number of cells expressing one or
                        more genes as a barplot
plot_spanning_tree      Plots the minimum spanning tree on cells.
reduceDimension         Computes a projection of a CellDataSet object
                        into a lower dimensional space
reducedDimA             Retrieves the weights that transform the cells'
                        coordinates in the reduced dimension space back
                        to the full (whitened) space.
reducedDimA<-           Sets the weights transform the cells'
                        coordinates in the reduced dimension space back
                        to the full (whitened) space.
reducedDimS             Retrieves the coordinates of each cell in the
                        reduced-dimensionality space generated by calls
                        to reduceDimension.
reducedDimS<-           Sets the coordinates of each cell in the
                        reduced-dimensionality space. Not intended to
                        be called directly.
reducedDimW             Retrieves the expression values for each cell
                        (as a matrix) after whitening during
                        independent component analysis.
reducedDimW<-           Sets the whitened expression values for each
                        cell prior to independent component analysis.
                        Not intended to be called directly.
responseMatrix          Response values
selectNegentropyGenes   Filter genes with extremely high or low
                        negentropy
setOrderingFilter       Sets the features (e.g. genes) to be used for
                        ordering cells in pseudotime.
