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

## Documentation for package ‘monocle’ version 2.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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