BEAM                    Branched expression analysis modeling (BEAM).
CellDataSet             The CellDataSet class
CellDataSet-methods     Methods for the CellDataSet class
CellType                The CellType class
CellTypeHierarchy       The CellTypeHierarchy class
addCellType             Add a new cell type
branchTest              Test for branch-dependent expression
buildBranchCellDataSet
                        Build a CellDataSet that splits cells among two
                        branches
calABCs                 Compute the area between curves (ABC) for
                        branch-dependent genes
calILRs                 Calculate the Instantaneous Log Ratio between
                        two branches
calibrate_per_cell_total_proposal
                        Calibrate_per_cell_total_proposal
cellPairwiseDistances   Get the matrix of pairwise distances between
                        cells
cellPairwiseDistances<-
                        Sets the matrix containing distances between
                        each pair of cells used by Monocle during cell
                        ordering. Not intended to be called directly.
clusterCells            Cluster cells into a specified number of groups
                        based on .
clusterGenes            Clusters genes by pseudotime trend.
compareModels           Compare model fits
detectBifurcationPoint
                        Calculate divergence times for branch-dependent
                        genes
detectGenes             Detects genes above minimum threshold.
diff_test_helper        Helper function for parallel differential
                        expression testing
differentialGeneTest    Test genes for differential expression
dispersionTable         Retrieve a table of values specifying the
                        mean-variance relationship
estimateDispersionsForCellDataSet
                        Helper function to estimate dispersions
estimateSizeFactorsForMatrix
                        Function to calculate the size factor for the
                        single-cell RNA-seq data @importFrom stats
                        median
estimate_t              Find the most commonly occuring relative
                        expression value in each cell
exportCDS               Export a monocle CellDataSet object to other
                        popular single cell analysis toolkit.
extract_good_branched_ordering
                        Extract a linear ordering of cells from a PQ
                        tree
fitModel                Fits a model for each gene in a CellDataSet
                        object.
fit_model_helper        Helper function for parallel VGAM fitting
genSmoothCurveResiduals
                        Fit smooth spline curves and return the
                        residuals matrix
genSmoothCurves         Fit smooth spline curves and return the
                        response matrix
get_classic_muscle_markers
                        Return the names of classic muscle genes
importCDS               Import a seurat or scatter/scran CellDataSet
                        object and convert it to a monocle cds.
load_HSMM               Build a CellDataSet from the HSMMSingleCell
                        package
load_HSMM_markers       Return a CellDataSet of classic muscle genes.
load_lung               Build a CellDataSet from the data stored in
                        inst/extdata directory.
markerDiffTable         Test genes for cell type-dependent expression
mcesApply               Multicore apply-like function for CellDataSet
minSpanningTree         Retrieves the minimum spanning tree generated
                        by Monocle during cell ordering.
minSpanningTree<-       Set the minimum spanning tree generated by
                        Monocle during cell ordering.
newCellDataSet          Creates a new CellDateSet object.
newCellTypeHierarchy    Classify cells according to a set of markers
orderCells              Orders cells according to pseudotime.
order_p_node            Return an ordering for a P node in the PQ tree
plot_cell_clusters      Plots clusters of cells .
plot_cell_trajectory    Plots the minimum spanning tree on cells.
plot_clusters           Plots kinetic clusters of genes.
plot_coexpression_matrix
                        Not sure we're ready to release this one quite
                        yet: Plot the branch genes in pseduotime with
                        separate branch curves
plot_complex_cell_trajectory
                        Plots the minimum spanning tree on cells.
plot_genes_branched_heatmap
                        Create a heatmap to demonstrate the bifurcation
                        of gene expression along two branchs
                        @description returns a heatmap that shows
                        changes in both lineages at the same time.  It
                        also requires that you choose a branch point to
                        inspect.  Columns are points in pseudotime,
                        rows are genes, and the beginning of pseudotime
                        is in the middle of the heatmap.  As you read
                        from the middle of the heatmap to the right,
                        you are following one lineage through
                        pseudotime. As you read left, the other.  The
                        genes are clustered hierarchically, so you can
                        visualize modules of genes that have similar
                        lineage-dependent expression patterns.
plot_genes_branched_pseudotime
                        Plot the branch genes in pseduotime with
                        separate branch curves.
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_genes_violin       Plots expression for one or more genes as a
                        violin plot
plot_multiple_branches_heatmap
                        Create a heatmap to demonstrate the bifurcation
                        of gene expression along multiple branches
plot_multiple_branches_pseudotime
                        Create a kinetic curves to demonstrate the
                        bifurcation of gene expression along multiple
                        branches
plot_ordering_genes     Plots genes by mean vs. dispersion,
                        highlighting those selected for ordering
plot_pc_variance_explained
                        Plots the percentage of variance explained by
                        the each component based on PCA from the
                        normalized expression data using the same
                        procedure used in reduceDimension function.
plot_pseudotime_heatmap
                        Plots a pseudotime-ordered, row-centered
                        heatmap
plot_rho_delta          Plots the decision map of density clusters .
plot_spanning_tree      Plots the minimum spanning tree on cells. This
                        function is deprecated.
pq_helper               Recursively builds and returns a PQ tree for
                        the MST
reduceDimension         Compute a projection of a CellDataSet object
                        into a lower dimensional space
reducedDimA             Get the weights needed to lift cells back to
                        high dimensional expression space.
reducedDimA<-           Get the weights needed to lift cells back to
                        high dimensional expression space.
reducedDimK             Retrieves the the whitening matrix during
                        independent component analysis.
reducedDimK<-           Sets the the whitening matrix during
                        independent component analysis.
reducedDimS             Retrieves the coordinates of each cell in the
                        reduced-dimensionality space generated by calls
                        to reduceDimension.
reducedDimS<-           Set embedding coordinates of each cell in a
                        CellDataSet.
reducedDimW             Get the whitened expression values for a
                        CellDataSet.
reducedDimW<-           Sets the whitened expression values for each
                        cell prior to independent component analysis.
                        Not intended to be called directly.
relative2abs            Transform relative expression values into
                        absolute transcript counts.
residualMatrix          Response values
responseMatrix          Calculates response values.
selectTopMarkers        Select the most cell type specific markers
setOrderingFilter       Marks genes for clustering
spike_df                Spike-in transcripts data.
vstExprs                Return a variance-stabilized matrix of
                        expression values
