Analysis tools for single-cell expression experiments.

Documentation for package ‘monocle’ version 1.0.0

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CellDataSet	The CellDataSet class
CellDataSet-class	The CellDataSet class
cellPairwiseDistances	Retrieves a matrix capturing distances between each cell in the reduced-dimensionality space
cellPairwiseDistances<-	Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.
clusterGenes	Plots the minimum spanning tree on cells.
compareModels	Compare model fits
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	Tests each gene for differential expression as a function of progress through a biological process, or according to other covariates as specified.
fitModel	Fits a model for each gene in a CellDataSet object.
minSpanningTree	Retrieves the minimum spanning tree generated by Monocle during cell ordering.
minSpanningTree<-	Sets the minimum spanning tree used by Monocle during cell ordering. Not intended to be called directly.
newCellDataSet	Creates a new CellDateSet object.
orderCells	Orders cells according to progress through a learned biological process.
plot_clusters	Plots the minimum spanning tree on cells.
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_spanning_tree	Plots the minimum spanning tree on cells.
reducedDimA	Retrieves the weights that transform the cells' coordinates in the reduced dimension space back to the full (whitened) space.
reducedDimA<-	Sets the weights transform the cells' coordinates in the reduced dimension space back to the full (whitened) space.
reducedDimS	Retrieves the coordinates of each cell in the reduced-dimensionality space generated by calls to reduceDimension.
reducedDimS<-	Sets the coordinates of each cell in the reduced-dimensionality space. Not intended to be called directly.
reducedDimW	Retrieves the expression values for each cell (as a matrix) after whitening during independent component analysis.
reducedDimW<-	Sets the whitened expression values for each cell prior to independent component analysis. Not intended to be called directly.
reduceDimension	Computes a projection of a CellDataSet object into a lower dimensional space
responseMatrix	Response values
selectNegentropyGenes	Filter genes with extremely high or low negentropy
setOrderingFilter	Sets the features (e.g. genes) to be used for ordering cells in pseudotime.