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The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class.
● Data Source:
BioConductor
● Keywords:
● Alias: CellDataSet, CellDataSet-class
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cellPairwiseDistances<-
(Package: monocle) :
Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.
Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.
● Data Source:
BioConductor
● Keywords:
● Alias: cellPairwiseDistances<-
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cellPairwiseDistances
(Package: monocle) :
Retrieves a matrix capturing distances between each cell in the reduced-dimensionality space
Retrieves a matrix capturing distances between each cell in the reduced-dimensionality space
● Data Source:
BioConductor
● Keywords:
● Alias: cellPairwiseDistances
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clusterGenes
(Package: monocle) :
Plots the minimum spanning tree on cells.
Plots the minimum spanning tree on cells.
● Data Source:
BioConductor
● Keywords:
● Alias: clusterGenes
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Performs likelihood ratio tests on nested vector generalized additive models
● Data Source:
BioConductor
● Keywords:
● Alias: compareModels
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detectGenes
(Package: monocle) :
Sets the global expression detection threshold to be used with this CellDataSet.
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.
● Data Source:
BioConductor
● Keywords:
● Alias: detectGenes
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differentialGeneTest
(Package: monocle) :
Tests each gene for differential expression as a function of progress through a biological process, or according to other covariates as specified.
Tests each gene for differential expression as a function of progress through a biological process, or according to other covariates as specified.
● Data Source:
BioConductor
● Keywords:
● Alias: differentialGeneTest
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fitModel
(Package: monocle) :
Fits a model for each gene in a CellDataSet object.
Fits a model for each gene in a CellDataSet object.
● Data Source:
BioConductor
● Keywords:
● Alias: fitModel
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minSpanningTree<-
(Package: monocle) :
Sets the minimum spanning tree used by Monocle during cell ordering. Not intended to be called directly.
Sets the minimum spanning tree used by Monocle during cell ordering. Not intended to be called directly.
● Data Source:
BioConductor
● Keywords:
● Alias: minSpanningTree<-
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minSpanningTree
(Package: monocle) :
Retrieve the minimum spanning tree generated by Monocle during cell ordering.
Retrieves the minimum spanning tree (MST) that Monocle constructs during orderCells(). This MST is mostly used in plot_spanning_tree to help assess the accuracy of Monocle's ordering.
● Data Source:
BioConductor
● Keywords:
● Alias: minSpanningTree
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providing 
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