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

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Documentation for package ‘monocle’ version 2.4.0

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addCellType Classify cells according to a set of markers
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 genes
calculateMarkerSpecificity Classify cells according to a set of markers
calibrate_per_cell_total_proposal Calibrate_per_cell_total_proposal
calILRs Calculate the Instantaneous Log Ratio between two branches
CellDataSet The CellDataSet class
CellDataSet-class The CellDataSet class
CellDataSet-method Methods for the CellDataSet class
CellDataSet-methods Methods for the CellDataSet class
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.
CellType The CellType class
CellType-class The CellType class
CellTypeHierarchy The CellTypeHierarchy class
CellTypeHierarchy-class The CellTypeHierarchy class
classifyCells Classify cells according to a set of markers
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 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 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 relationship
estimateDispersions-method Methods for the CellDataSet class
estimateDispersionsForCellDataSet Helper function to estimate dispersions
estimateSizeFactors-method Methods for the CellDataSet class
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
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
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_genes_branched_heatmap Create a heatmap to demonstrate the bifurcation of gene expression along two branchs
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_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
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.
reduceDimension Compute a projection of a CellDataSet object into a lower dimensional space
relative2abs Transform relative expression values into absolute transcript counts.
residualMatrix Response values
responseMatrix Response values
selectNegentropyGenes Filter genes with extremely high or low negentropy
selectTopMarkers Select the most cell type specific markers
setOrderingFilter Sets the features (e.g. genes) to be used for ordering cells in pseudotime.
sizeFactors-method Methods for the CellDataSet class
sizeFactors<--method Methods for the CellDataSet class
spike_df Spike-in transcripts data.
SubSet_cds Subset a cds which only includes cells provided with the argument cells
vstExprs Return a variance-stabilized matrix of expression values