addCellType	newCellTypeHierarchy
BEAM	BEAM
branchTest	branchTest
buildBranchCellDataSet	buildBranchCellDataSet
calABCs	calABCs
calculateMarkerSpecificity	newCellTypeHierarchy
calibrate_per_cell_total_proposal	calibrate_per_cell_total_proposal
calILRs	calILRs
CellDataSet	CellDataSet
CellDataSet,ANY,ANY-method	CellDataSet-methods
CellDataSet-class	CellDataSet
CellDataSet-methods	CellDataSet-methods
cellPairwiseDistances	cellPairwiseDistances
cellPairwiseDistances<-	cellPairwiseDistances-set
CellType	CellType
CellType-class	CellType
CellTypeHierarchy	CellTypeHierarchy
CellTypeHierarchy-class	CellTypeHierarchy
classifyCells	newCellTypeHierarchy
clusterCells	clusterCells
clusterGenes	clusterGenes
compareModels	compareModels
detectBifurcationPoint	detectBifurcationPoint
detectGenes	detectGenes
differentialGeneTest	differentialGeneTest
diff_test_helper	diff_test_helper
dispersionTable	dispersionTable
estimateDispersions,CellDataSet-method	CellDataSet-methods
estimateDispersionsForCellDataSet	estimateDispersionsForCellDataSet
estimateSizeFactors,CellDataSet-method	CellDataSet-methods
estimateSizeFactorsForMatrix	estimateSizeFactorsForMatrix
estimate_t	estimate_t
extract_good_branched_ordering	extract_good_branched_ordering
fitModel	fitModel
fit_model_helper	fit_model_helper
genSmoothCurveResiduals	genSmoothCurveResiduals
genSmoothCurves	genSmoothCurves
get_classic_muscle_markers	get_classic_muscle_markers
load_HSMM	load_HSMM
load_HSMM_markers	load_HSMM_markers
load_lung	load_lung
markerDiffTable	markerDiffTable
mcesApply	mcesApply
minSpanningTree	minSpanningTree
minSpanningTree<-	minSpanningTree-set
newCellDataSet	newCellDataSet
newCellTypeHierarchy	newCellTypeHierarchy
orderCells	orderCells
order_p_node	order_p_node
plot_cell_clusters	plot_cell_clusters
plot_cell_trajectory	plot_cell_trajectory
plot_clusters	plot_clusters
plot_coexpression_matrix	plot_coexpression_matrix
plot_genes_branched_heatmap	plot_genes_branched_heatmap
plot_genes_branched_pseudotime	plot_genes_branched_pseudotime
plot_genes_in_pseudotime	plot_genes_in_pseudotime
plot_genes_jitter	plot_genes_jitter
plot_genes_positive_cells	plot_genes_positive_cells
plot_ordering_genes	plot_ordering_genes
plot_pc_variance_explained	plot_pc_variance_explained
plot_pseudotime_heatmap	plot_pseudotime_heatmap
plot_rho_delta	plot_rho_delta
plot_spanning_tree	package-deprecated
pq_helper	pq_helper
reducedDimA	reducedDimA
reducedDimA<-	reducedDimA-set
reducedDimK	reducedDimK
reducedDimK<-	reducedDimK-set
reducedDimS	reducedDimS
reducedDimS<-	reducedDimS-set
reducedDimW	reducedDimW
reducedDimW<-	reducedDimW-set
reduceDimension	reduceDimension
relative2abs	relative2abs
residualMatrix	residualMatrix
responseMatrix	responseMatrix
selectNegentropyGenes	selectNegentropyGenes
selectTopMarkers	selectTopMarkers
setOrderingFilter	setOrderingFilter
sizeFactors,CellDataSet-method	CellDataSet-methods
sizeFactors<-,CellDataSet,numeric-method	CellDataSet-methods
spike_df	spike_df
SubSet_cds	SubSet_cds
vstExprs	vstExprs
