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 |
Retrieve 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 |
Get the weights needed to lift cells back to high dimensional expression space. |
reducedDimA<- |
Get the weights needed to lift cells back to high dimensional expression space. |
reducedDimS |
Retrieves the coordinates of each cell in the reduced-dimensionality space generated by calls to reduceDimension. |
reducedDimS<- |
Set embedding coordinates of each cell in a CellDataSet. |
reducedDimW |
Get the whitened expression values for a CellDataSet. |
reducedDimW<- |
Get the whitened expression values for a CellDataSet. |
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. |