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

## Documentation for package ‘monocle’ version 2.22.0

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

## Help Pages

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 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 | 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 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
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
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 | Calculates response values.
selectTopMarkers | Select the most cell type specific markers
setOrderingFilter | Marks genes for clustering
sizeFactors-method | Methods for the CellDataSet class
sizeFactors<--method | Methods for the CellDataSet class
spike_df | Spike-in transcripts data.
vstExprs | Return a variance-stabilized matrix of expression values