Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

addCellType | Add a new cell type |

BEAM | Branched expression analysis modeling (BEAM). |

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... |

calibrate_per_cell_total_proposal | Calibrate_per_cell_total_proposal |

calILRs | Calculate the Instantaneous Log Ratio between two branches |

CellDataSet | The CellDataSet class |

CellDataSet-methods | Methods for the CellDataSet class |

cellPairwiseDistances | Get the matrix of pairwise distances between cells |

cellPairwiseDistances-set | Sets the matrix containing distances between each pair of... |

CellType | The CellType class |

CellTypeHierarchy | The CellTypeHierarchy class |

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. |

differentialGeneTest | Test genes for differential expression |

diff_test_helper | Helper function for parallel differential expression testing |

dispersionTable | Retrieve a table of values specifying the mean-variance... |

estimateDispersionsForCellDataSet | Helper function to estimate dispersions |

estimateSizeFactorsForMatrix | Function to calculate the size factor for the single-cell... |

estimate_t | Find the most commonly occuring relative expression value in... |

exportCDS | Export a monocle CellDataSet object to other popular single... |

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... |

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... |

markerDiffTable | Test genes for cell type-dependent expression |

mcesApply | Multicore apply-like function for CellDataSet |

minSpanningTree | Retrieves the minimum spanning tree generated by Monocle... |

minSpanningTree-set | Set the minimum spanning tree generated by Monocle during... |

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 |

package-deprecated | Plots the minimum spanning tree on cells. This function is... |

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... |

plot_complex_cell_trajectory | Plots the minimum spanning tree on cells. |

plot_genes_branched_heatmap | Create a heatmap to demonstrate the bifurcation of gene... |

plot_genes_branched_pseudotime | Plot the branch genes in pseduotime with separate branch... |

plot_genes_in_pseudotime | Plots expression for one or more genes as a function of... |

plot_genes_jitter | Plots expression for one or more genes as a jittered, grouped... |

plot_genes_positive_cells | Plots the number of cells expressing one or more genes as a... |

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... |

plot_multiple_branches_pseudotime | Create a kinetic curves to demonstrate the bifurcation of... |

plot_ordering_genes | Plots genes by mean vs. dispersion, highlighting those... |

plot_pc_variance_explained | Plots the percentage of variance explained by the each... |

plot_pseudotime_heatmap | Plots a pseudotime-ordered, row-centered heatmap |

plot_rho_delta | Plots the decision map of density clusters . |

pq_helper | Recursively builds and returns a PQ tree for the MST |

reducedDimA | Get the weights needed to lift cells back to high dimensional... |

reducedDimA-set | Get the weights needed to lift cells back to high dimensional... |

reducedDimK | Retrieves the the whitening matrix during independent... |

reducedDimK-set | Sets the the whitening matrix during independent component... |

reducedDimS | Retrieves the coordinates of each cell in the... |

reducedDimS-set | Set embedding coordinates of each cell in a CellDataSet. |

reducedDimW | Get the whitened expression values for a CellDataSet. |

reducedDimW-set | Sets the whitened expression values for each cell prior to... |

reduceDimension | Compute a projection of a CellDataSet object into a lower... |

relative2abs | Transform relative expression values into absolute transcript... |

residualMatrix | Response values |

responseMatrix | Calculates response values. |

selectNegentropyGenes | Filter genes with extremely high or low negentropy |

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 |

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