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"calABCs" ] }, { "page": "calibrate_per_cell_total_proposal", "title": "Calibrate_per_cell_total_proposal", "topics": [ "calibrate_per_cell_total_proposal" ] }, { "page": "calILRs", "title": "Calculate the Instantaneous Log Ratio between two branches", "topics": [ "calILRs" ] }, { "page": "CellDataSet", "title": "The CellDataSet class", "topics": [ "CellDataSet", "CellDataSet-class" ] }, { "page": "CellDataSet-methods", "title": "Methods for the CellDataSet class", "topics": [ "CellDataSet,ANY,ANY-method", "CellDataSet-methods", "estimateDispersions,CellDataSet-method", "estimateSizeFactors,CellDataSet-method", "sizeFactors,CellDataSet-method", "sizeFactors<-,CellDataSet,numeric-method" ] }, { "page": "cellPairwiseDistances", "title": "Get the matrix of pairwise distances between cells", "topics": [ "cellPairwiseDistances" ] }, { "page": "cellPairwiseDistances-set", "title": "Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.", "topics": [ "cellPairwiseDistances<-" ] }, { "page": "CellType", "title": "The CellType class", "topics": [ "CellType", "CellType-class" ] }, { "page": "CellTypeHierarchy", "title": "The CellTypeHierarchy class", "topics": [ "CellTypeHierarchy", "CellTypeHierarchy-class" ] }, { "page": "clusterCells", "title": "Cluster cells into a specified number of groups based on .", "topics": [ "clusterCells" ] }, { "page": "clusterGenes", "title": "Clusters genes by pseudotime trend.", "topics": [ "clusterGenes" ] }, { "page": "compareModels", "title": "Compare model fits", "topics": [ "compareModels" ] }, { "page": "detectBifurcationPoint", "title": "Calculate divergence times for branch-dependent genes", "topics": [ "detectBifurcationPoint" ] }, { "page": "detectGenes", "title": "Detects genes above minimum threshold.", "topics": [ "detectGenes" ] }, { "page": "diff_test_helper", "title": "Helper function for parallel differential expression testing", "topics": [ "diff_test_helper" ] }, { "page": "differentialGeneTest", "title": "Test genes for differential expression", "topics": [ "differentialGeneTest" ] }, { "page": "dispersionTable", "title": "Retrieve a table of values specifying the mean-variance relationship", "topics": [ "dispersionTable" ] }, { "page": "estimate_t", "title": "Find the most commonly occuring relative expression value in each cell", "topics": [ "estimate_t" ] }, { "page": "estimateDispersionsForCellDataSet", "title": "Helper function to estimate dispersions", "topics": [ "estimateDispersionsForCellDataSet" ] }, { "page": "estimateSizeFactorsForMatrix", "title": "Function to calculate the size factor for the single-cell RNA-seq data @importFrom stats median", "topics": [ "estimateSizeFactorsForMatrix" ] }, { "page": "exportCDS", "title": "Export a monocle CellDataSet object to the Seurat single cell analysis toolkit.", "topics": [ "exportCDS" ] }, { "page": "extract_good_branched_ordering", "title": "Extract a linear ordering of cells from a PQ tree", "topics": [ "extract_good_branched_ordering" ] }, { "page": "fit_model_helper", "title": "Helper function for parallel VGAM fitting", "topics": [ "fit_model_helper" ] }, { "page": "fitModel", "title": "Fits a model for each gene in a CellDataSet object.", "topics": [ "fitModel" ] }, { "page": "genSmoothCurveResiduals", "title": "Fit smooth spline curves and return the residuals matrix", "topics": [ "genSmoothCurveResiduals" ] }, { "page": "genSmoothCurves", "title": "Fit smooth spline curves and return the response matrix", "topics": [ "genSmoothCurves" ] }, { "page": "get_classic_muscle_markers", "title": "Return the names of classic muscle genes", "topics": [ "get_classic_muscle_markers" ] }, { "page": "importCDS", "title": "Import a Seurat object and convert it to a monocle cds.", "topics": [ "importCDS" ] }, { "page": "load_HSMM", "title": "Build a CellDataSet from the HSMMSingleCell package", "topics": [ "load_HSMM" ] }, { "page": "load_HSMM_markers", "title": "Return a CellDataSet of classic muscle genes.", "topics": [ "load_HSMM_markers" ] }, { "page": "load_lung", "title": "Build a CellDataSet from the data stored in inst/extdata directory.", "topics": [ "load_lung" ] }, { "page": "markerDiffTable", "title": "Test genes for cell type-dependent expression", "topics": [ "markerDiffTable" ] }, { "page": "mcesApply", "title": "Multicore apply-like function for CellDataSet", "topics": [ "mcesApply" ] }, { "page": "minSpanningTree", "title": "Retrieves the minimum spanning tree generated by Monocle during cell ordering.", "topics": [ "minSpanningTree" ] }, { "page": "minSpanningTree-set", "title": "Set the minimum spanning tree generated by Monocle during cell ordering.", "topics": [ "minSpanningTree<-" ] }, { "page": "newCellDataSet", "title": "Creates a new CellDateSet object.", "topics": [ "newCellDataSet" ] }, { "page": "newCellTypeHierarchy", "title": "Classify cells according to a set of markers", "topics": [ "calculateMarkerSpecificity", "classifyCells", "newCellTypeHierarchy" ] }, { "page": "order_p_node", "title": "Return an ordering for a P node in the PQ tree", "topics": [ "order_p_node" ] }, { "page": "orderCells", "title": "Orders cells according to pseudotime.", "topics": [ "orderCells" ] }, { "page": "plot_cell_clusters", "title": "Plots clusters of cells .", "topics": [ "plot_cell_clusters" ] }, { "page": "plot_cell_trajectory", "title": "Plots the minimum spanning tree on cells.", "topics": [ "plot_cell_trajectory" ] }, { "page": "plot_clusters", "title": "Plots kinetic clusters of genes.", "topics": [ "plot_clusters" ] }, { "page": "plot_coexpression_matrix", "title": "Not sure we're ready to release this one quite yet: Plot the branch genes in pseduotime with separate branch curves", "topics": [ "plot_coexpression_matrix" ] }, { "page": "plot_complex_cell_trajectory", "title": "Plots the minimum spanning tree on cells.", "topics": [ "plot_complex_cell_trajectory" ] }, { "page": "plot_genes_branched_heatmap", "title": "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.", "topics": [ "plot_genes_branched_heatmap" ] }, { "page": "plot_genes_branched_pseudotime", "title": "Plot the branch genes in pseduotime with separate branch curves.", "topics": [ "plot_genes_branched_pseudotime" ] }, { "page": "plot_genes_in_pseudotime", "title": "Plots expression for one or more genes as a function of pseudotime", "topics": [ "plot_genes_in_pseudotime" ] }, { "page": "plot_genes_jitter", "title": "Plots expression for one or more genes as a jittered, grouped points", "topics": [ "plot_genes_jitter" ] }, { "page": "plot_genes_positive_cells", "title": "Plots the number of cells expressing one or more genes as a barplot", "topics": [ "plot_genes_positive_cells" ] }, { "page": "plot_genes_violin", "title": "Plots expression for one or more genes as a violin plot", "topics": [ "plot_genes_violin" ] }, { "page": "plot_multiple_branches_heatmap", "title": "Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches", "topics": [ "plot_multiple_branches_heatmap" ] }, { "page": "plot_multiple_branches_pseudotime", "title": "Create a kinetic curves to demonstrate the bifurcation of gene expression along multiple branches", "topics": [ "plot_multiple_branches_pseudotime" ] }, { "page": "plot_ordering_genes", "title": "Plots genes by mean vs. dispersion, highlighting those selected for ordering", "topics": [ "plot_ordering_genes" ] }, { "page": "plot_pc_variance_explained", "title": "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.", "topics": [ "plot_pc_variance_explained" ] }, { "page": "plot_pseudotime_heatmap", "title": "Plots a pseudotime-ordered, row-centered heatmap", "topics": [ "plot_pseudotime_heatmap" ] }, { "page": "plot_rho_delta", "title": "Plots the decision map of density clusters .", "topics": [ "plot_rho_delta" ] }, { "page": "package-deprecated", "title": "Plots the minimum spanning tree on cells. This function is deprecated.", "topics": [ "plot_spanning_tree" ] }, { "page": "pq_helper", "title": "Recursively builds and returns a PQ tree for the MST", "topics": [ "pq_helper" ] }, { "page": "reducedDimA", "title": "Get the weights needed to lift cells back to high dimensional expression space.", "topics": [ "reducedDimA" ] }, { "page": "reducedDimA-set", "title": "Get the weights needed to lift cells back to high dimensional expression space.", "topics": [ "reducedDimA<-" ] }, { "page": "reducedDimK", "title": "Retrieves the the whitening matrix during independent component analysis.", "topics": [ "reducedDimK" ] }, { "page": "reducedDimK-set", "title": "Sets the the whitening matrix during independent component analysis.", "topics": [ "reducedDimK<-" ] }, { "page": "reducedDimS", "title": "Retrieves the coordinates of each cell in the reduced-dimensionality space generated by calls to reduceDimension.", "topics": [ "reducedDimS" ] }, { "page": "reducedDimS-set", "title": "Set embedding coordinates of each cell in a CellDataSet.", "topics": [ "reducedDimS<-" ] }, { "page": "reducedDimW", "title": "Get the whitened expression values for a CellDataSet.", "topics": [ "reducedDimW" ] }, { "page": "reducedDimW-set", "title": "Sets the whitened expression values for each cell prior to independent component analysis. Not intended to be called directly.", "topics": [ "reducedDimW<-" ] }, { "page": "reduceDimension", "title": "Compute a projection of a CellDataSet object into a lower dimensional space", "topics": [ "reduceDimension" ] }, { "page": "relative2abs", "title": "Transform relative expression values into absolute transcript counts.", "topics": [ "relative2abs" ] }, { "page": "residualMatrix", "title": "Response values", "topics": [ "residualMatrix" ] }, { "page": "responseMatrix", "title": "Calculates response values.", "topics": [ "responseMatrix" ] }, { "page": "selectTopMarkers", "title": "Select the most cell type specific markers", "topics": [ "selectTopMarkers" ] }, { "page": "setOrderingFilter", "title": "Marks genes for clustering", "topics": [ "setOrderingFilter" ] }, { "page": "spike_df", "title": "Spike-in transcripts data.", "topics": [ "spike_df" ] }, { "page": "vstExprs", "title": "Return a variance-stabilized matrix of expression values", "topics": [ "vstExprs" ] } ], 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