Man pages for cole-trapnell-lab/monocle-release
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

addCellTypeAdd a new cell type
BEAMBranched expression analysis modeling (BEAM).
branchTestTest for branch-dependent expression
buildBranchCellDataSetBuild a CellDataSet that splits cells among two branches
calABCsCompute the area between curves (ABC) for branch-dependent...
calibrate_per_cell_total_proposalCalibrate_per_cell_total_proposal
calILRsCalculate the Instantaneous Log Ratio between two branches
CellDataSetThe CellDataSet class
CellDataSet-methodsMethods for the CellDataSet class
cellPairwiseDistancesGet the matrix of pairwise distances between cells
cellPairwiseDistances-setSets the matrix containing distances between each pair of...
CellTypeThe CellType class
CellTypeHierarchyThe CellTypeHierarchy class
clusterCellsCluster cells into a specified number of groups based on .
clusterGenesClusters genes by pseudotime trend.
compareModelsCompare model fits
detectBifurcationPointCalculate divergence times for branch-dependent genes
detectGenesDetects genes above minimum threshold.
differentialGeneTestTest genes for differential expression
diff_test_helperHelper function for parallel differential expression testing
dispersionTableRetrieve a table of values specifying the mean-variance...
estimateDispersionsForCellDataSetHelper function to estimate dispersions
estimateSizeFactorsForMatrixFunction to calculate the size factor for the single-cell...
estimate_tFind the most commonly occuring relative expression value in...
exportCDSExport a monocle CellDataSet object to other popular single...
extract_good_branched_orderingExtract a linear ordering of cells from a PQ tree
fitModelFits a model for each gene in a CellDataSet object.
fit_model_helperHelper function for parallel VGAM fitting
genSmoothCurveResidualsFit smooth spline curves and return the residuals matrix
genSmoothCurvesFit smooth spline curves and return the response matrix
get_classic_muscle_markersReturn the names of classic muscle genes
importCDSImport a seurat or scatter/scran CellDataSet object and...
load_HSMMBuild a CellDataSet from the HSMMSingleCell package
load_HSMM_markersReturn a CellDataSet of classic muscle genes.
load_lungBuild a CellDataSet from the data stored in inst/extdata...
markerDiffTableTest genes for cell type-dependent expression
mcesApplyMulticore apply-like function for CellDataSet
minSpanningTreeRetrieves the minimum spanning tree generated by Monocle...
minSpanningTree-setSet the minimum spanning tree generated by Monocle during...
newCellDataSetCreates a new CellDateSet object.
newCellTypeHierarchyClassify cells according to a set of markers
orderCellsOrders cells according to pseudotime.
order_p_nodeReturn an ordering for a P node in the PQ tree
package-deprecatedPlots the minimum spanning tree on cells. This function is...
plot_cell_clustersPlots clusters of cells .
plot_cell_trajectoryPlots the minimum spanning tree on cells.
plot_clustersPlots kinetic clusters of genes.
plot_coexpression_matrixNot sure we're ready to release this one quite yet: Plot the...
plot_complex_cell_trajectoryPlots the minimum spanning tree on cells.
plot_genes_branched_heatmapCreate a heatmap to demonstrate the bifurcation of gene...
plot_genes_branched_pseudotimePlot the branch genes in pseduotime with separate branch...
plot_genes_in_pseudotimePlots expression for one or more genes as a function of...
plot_genes_jitterPlots expression for one or more genes as a jittered, grouped...
plot_genes_positive_cellsPlots the number of cells expressing one or more genes as a...
plot_genes_violinPlots expression for one or more genes as a violin plot
plot_multiple_branches_heatmapCreate a heatmap to demonstrate the bifurcation of gene...
plot_multiple_branches_pseudotimeCreate a kinetic curves to demonstrate the bifurcation of...
plot_ordering_genesPlots genes by mean vs. dispersion, highlighting those...
plot_pc_variance_explainedPlots the percentage of variance explained by the each...
plot_pseudotime_heatmapPlots a pseudotime-ordered, row-centered heatmap
plot_rho_deltaPlots the decision map of density clusters .
pq_helperRecursively builds and returns a PQ tree for the MST
reducedDimAGet the weights needed to lift cells back to high dimensional...
reducedDimA-setGet the weights needed to lift cells back to high dimensional...
reducedDimKRetrieves the the whitening matrix during independent...
reducedDimK-setSets the the whitening matrix during independent component...
reducedDimSRetrieves the coordinates of each cell in the...
reducedDimS-setSet embedding coordinates of each cell in a CellDataSet.
reducedDimWGet the whitened expression values for a CellDataSet.
reducedDimW-setSets the whitened expression values for each cell prior to...
reduceDimensionCompute a projection of a CellDataSet object into a lower...
relative2absTransform relative expression values into absolute transcript...
residualMatrixResponse values
responseMatrixCalculates response values.
selectNegentropyGenesFilter genes with extremely high or low negentropy
selectTopMarkersSelect the most cell type specific markers
setOrderingFilterMarks genes for clustering
spike_dfSpike-in transcripts data.
vstExprsReturn a variance-stabilized matrix of expression values
cole-trapnell-lab/monocle-release documentation built on Nov. 21, 2017, 6:49 a.m.