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monocle (version 1.6.2)

Analysis tools for single-cell expression experiments.

Description

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

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Version

Version

1.6.2

License

Artistic-2.0

Maintainer

Cole Trapnell

Last Published

February 15th, 2017

Functions in monocle (1.6.2)

plot_spanning_tree

Plots the minimum spanning tree on cells.
reducedDimW<-

Get the whitened expression values for a CellDataSet.
newCellDataSet

Creates a new CellDateSet object.
plot_genes_in_pseudotime

Plots expression for one or more genes as a function of pseudotime
cellPairwiseDistances<-

Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.
reducedDimS<-

Set embedding coordinates of each cell in a CellDataSet.
compareModels

Compare model fits
selectNegentropyGenes

Filter genes with extremely high or low negentropy
reducedDimA

Get the weights needed to lift cells back to high dimensional expression space.
cellPairwiseDistances

Retrieves a matrix capturing distances between each cell in the reduced-dimensionality space
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.
reducedDimS

Retrieves the coordinates of each cell in the reduced-dimensionality space generated by calls to reduceDimension.
setOrderingFilter

Sets the features (e.g. genes) to be used for ordering cells in pseudotime.
minSpanningTree<-

Sets the minimum spanning tree used by Monocle during cell ordering. Not intended to be called directly.
responseMatrix

Response values
clusterGenes

Plots the minimum spanning tree on cells.
reducedDimW

Get the whitened expression values for a CellDataSet.
orderCells

Orders cells according to progress through a learned biological process.
reduceDimension

Computes a projection of a CellDataSet object into a lower dimensional space
plot_genes_positive_cells

Plots the number of cells expressing one or more genes as a barplot
differentialGeneTest

Tests each gene for differential expression as a function of progress through a biological process, or according to other covariates as specified.
plot_genes_jitter

Plots expression for one or more genes as a jittered, grouped points
CellDataSet

The CellDataSet class
fitModel

Fits a model for each gene in a CellDataSet object.
minSpanningTree

Retrieve the minimum spanning tree generated by Monocle during cell ordering.
reducedDimA<-

Get the weights needed to lift cells back to high dimensional expression space.
plot_clusters

Plots the minimum spanning tree on cells.