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.
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 Oct. 18, 2018, 4:18 a.m.