monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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.

Author
Cole Trapnell
Date of publication
None
Maintainer
Cole Trapnell <coletrap@uw.edu>
License
Artistic-2.0
Version
2.2.0

View on Bioconductor

Man pages

BEAM
Branched expression analysis modeling (BEAM)
branchTest
Test for branch-dependent expression
buildBranchCellDataSet
Build a CellDataSet that splits cells among two branches
calABCs
Compute the area between curves (ABC) for branch-dependent...
calibrate_per_cell_total_proposal
Calibrate_per_cell_total_proposal
calILRs
Calculate the Instantaneous Log Ratio between two branches
CellDataSet
The CellDataSet class
CellDataSet-methods
Methods for the CellDataSet class
cellPairwiseDistances
Get the matrix of pairwise distances between cells
cellPairwiseDistances-set
Sets the matrix containing distances between each pair of...
CellType
The CellType class
CellTypeHierarchy
The CellTypeHierarchy class
clusterCells
Cluster cells into a specified number of groups.
clusterGenes
Clusters genes by pseudotime trend.
compareModels
Compare model fits
detectBifurcationPoint
Calculate divergence times for branch-dependent genes
detectGenes
Sets the global expression detection threshold to be used...
differentialGeneTest
Test genes for differential expression
diff_test_helper
Helper function for parallel differential expression testing
dispersionTable
Retrieve a table of values specifying the mean-variance...
estimateDispersionsForCellDataSet
Helper function to estimate dispersions
estimateSizeFactorsForMatrix
Function to calculate the size factor for the single-cell...
estimate_t
Find the most commonly occuring relative expression value in...
extract_good_branched_ordering
Extract a linear ordering of cells from a PQ tree
fitModel
Fits a model for each gene in a CellDataSet object.
fit_model_helper
Helper function for parallel VGAM fitting
genSmoothCurveResiduals
Fit smooth spline curves and return the residuals matrix
genSmoothCurves
Fit smooth spline curves and return the response matrix
get_classic_muscle_markers
Return the names of classic muscle genes
load_HSMM
Build a CellDataSet from the HSMMSingleCell package
load_HSMM_markers
Return a CellDataSet of classic muscle genes
load_lung
Build a CellDataSet from the data stored in inst/extdata...
markerDiffTable
Test genes for cell type-dependent expression
mcesApply
Multicore apply-like function for CellDataSet
minSpanningTree
Retrieves the minimum spanning tree generated by Monocle...
minSpanningTree-set
Set the minimum spanning tree generated by Monocle during...
newCellDataSet
Creates a new CellDateSet object.
newCellTypeHierarchy
Classify cells according to a set of markers
orderCells
Orders cells according to pseudotime.
order_p_node
Return an ordering for a P node in the PQ tree
package-deprecated
Plots the minimum spanning tree on cells. This function is...
plot_cell_trajectory
Plots the minimum spanning tree on cells.
plot_clusters
Plots kinetic clusters of genes.
plot_coexpression_matrix
Not sure we're ready to release this one quite yet: Plot the...
plot_genes_branched_heatmap
Create a heatmap to demonstrate the bifurcation of gene...
plot_genes_branched_pseudotime
Plot the branch genes in pseduotime with separate branch...
plot_genes_in_pseudotime
Plots expression for one or more genes as a function of...
plot_genes_jitter
Plots expression for one or more genes as a jittered, grouped...
plot_genes_positive_cells
Plots the number of cells expressing one or more genes as a...
plot_ordering_genes
Plots genes by mean vs. dispersion, highlighting those...
plot_pseudotime_heatmap
Plots a pseudotime-ordered, row-centered heatmap
pq_helper
Recursively builds and returns a PQ tree for the MST
reducedDimA
Get the weights needed to lift cells back to high dimensional...
reducedDimA-set
Get the weights needed to lift cells back to high dimensional...
reducedDimK
Retrieves the the whitening matrix during independent...
reducedDimK-set
Sets the the whitening matrix during independent component...
reducedDimS
Retrieves the coordinates of each cell in the...
reducedDimS-set
Set embedding coordinates of each cell in a CellDataSet.
reducedDimW
Get the whitened expression values for a CellDataSet.
reducedDimW-set
Sets the whitened expression values for each cell prior to...
reduceDimension
Compute a projection of a CellDataSet object into a lower...
relative2abs
Transform relative expression values into absolute transcript...
residualMatrix
Response values
responseMatrix
Response values
scale_pseudotime
Scale pseudotime to be in the range from 0 to 100
selectNegentropyGenes
Filter genes with extremely high or low negentropy
selectTopMarkers
Select the most cell type specific markers
setOrderingFilter
Sets the features (e.g. genes) to be used for ordering cells...
spike_df
Spike-in transcripts data.
vstExprs
Return a variance-stabilized matrix of expression values

Files in this package

monocle/DESCRIPTION
monocle/NAMESPACE
monocle/NEWS
monocle/R
monocle/R/BEAM.R
monocle/R/CellDataSet.R
monocle/R/CellType.R
monocle/R/CellTypeHierarchy.R
monocle/R/cluster_cells.R
monocle/R/clustering.R
monocle/R/data_sets.R
monocle/R/differential_expression.R
monocle/R/expr_models.R
monocle/R/methods-CellDataSet.R
monocle/R/methods-CellTypeHierarchy.R
monocle/R/normalization.R
monocle/R/order_cells.R
monocle/R/plotting.R
monocle/R/utils.R
monocle/README
monocle/build
monocle/build/vignette.rds
monocle/data
monocle/data/spike_df.rda
monocle/examples
monocle/examples/HSMM_analysis.R
monocle/inst
monocle/inst/CITATION
monocle/inst/doc
monocle/inst/doc/monocle-vignette.R
monocle/inst/doc/monocle-vignette.Rnw
monocle/inst/doc/monocle-vignette.pdf
monocle/inst/extdata
monocle/inst/extdata/lung_exprs_data.RData
monocle/inst/extdata/lung_feature_data.RData
monocle/inst/extdata/lung_phenotype_data.RData
monocle/inst/tests
monocle/inst/tests/basic_tests.R
monocle/man
monocle/man/BEAM.Rd
monocle/man/CellDataSet-methods.Rd
monocle/man/CellDataSet.Rd
monocle/man/CellType.Rd
monocle/man/CellTypeHierarchy.Rd
monocle/man/branchTest.Rd
monocle/man/buildBranchCellDataSet.Rd
monocle/man/calABCs.Rd
monocle/man/calILRs.Rd
monocle/man/calibrate_per_cell_total_proposal.Rd
monocle/man/cellPairwiseDistances-set.Rd
monocle/man/cellPairwiseDistances.Rd
monocle/man/clusterCells.Rd
monocle/man/clusterGenes.Rd
monocle/man/compareModels.Rd
monocle/man/detectBifurcationPoint.Rd
monocle/man/detectGenes.Rd
monocle/man/diff_test_helper.Rd
monocle/man/differentialGeneTest.Rd
monocle/man/dispersionTable.Rd
monocle/man/estimateDispersionsForCellDataSet.Rd
monocle/man/estimateSizeFactorsForMatrix.Rd
monocle/man/estimate_t.Rd
monocle/man/extract_good_branched_ordering.Rd
monocle/man/fitModel.Rd
monocle/man/fit_model_helper.Rd
monocle/man/genSmoothCurveResiduals.Rd
monocle/man/genSmoothCurves.Rd
monocle/man/get_classic_muscle_markers.Rd
monocle/man/load_HSMM.Rd
monocle/man/load_HSMM_markers.Rd
monocle/man/load_lung.Rd
monocle/man/markerDiffTable.Rd
monocle/man/mcesApply.Rd
monocle/man/minSpanningTree-set.Rd
monocle/man/minSpanningTree.Rd
monocle/man/newCellDataSet.Rd
monocle/man/newCellTypeHierarchy.Rd
monocle/man/orderCells.Rd
monocle/man/order_p_node.Rd
monocle/man/package-deprecated.Rd
monocle/man/plot_cell_trajectory.Rd
monocle/man/plot_clusters.Rd
monocle/man/plot_coexpression_matrix.Rd
monocle/man/plot_genes_branched_heatmap.Rd
monocle/man/plot_genes_branched_pseudotime.Rd
monocle/man/plot_genes_in_pseudotime.Rd
monocle/man/plot_genes_jitter.Rd
monocle/man/plot_genes_positive_cells.Rd
monocle/man/plot_ordering_genes.Rd
monocle/man/plot_pseudotime_heatmap.Rd
monocle/man/pq_helper.Rd
monocle/man/reduceDimension.Rd
monocle/man/reducedDimA-set.Rd
monocle/man/reducedDimA.Rd
monocle/man/reducedDimK-set.Rd
monocle/man/reducedDimK.Rd
monocle/man/reducedDimS-set.Rd
monocle/man/reducedDimS.Rd
monocle/man/reducedDimW-set.Rd
monocle/man/reducedDimW.Rd
monocle/man/relative2abs.Rd
monocle/man/residualMatrix.Rd
monocle/man/responseMatrix.Rd
monocle/man/scale_pseudotime.Rd
monocle/man/selectNegentropyGenes.Rd
monocle/man/selectTopMarkers.Rd
monocle/man/setOrderingFilter.Rd
monocle/man/spike_df.Rd
monocle/man/vstExprs.Rd
monocle/tests
monocle/tests/testthat
monocle/tests/testthat.R
monocle/tests/testthat/test.BEAM.R
monocle/tests/testthat/test.CellDataSet-setup.R
monocle/tests/testthat/test.branchTest.R
monocle/tests/testthat/test.buildLineageBranchCellDataSet.R
monocle/tests/testthat/test.calIABCs.R
monocle/tests/testthat/test.calILRs.R
monocle/tests/testthat/test.cellPairwiseDistances.R
monocle/tests/testthat/test.clusterCells.R
monocle/tests/testthat/test.clusterGenes.R
monocle/tests/testthat/test.compareModels.R
monocle/tests/testthat/test.detectBifurcationPoint.R
monocle/tests/testthat/test.detectGenes.R
monocle/tests/testthat/test.differentialExpression.R
monocle/tests/testthat/test.estimateDispersion.R
monocle/tests/testthat/test.estimate_t.R
monocle/tests/testthat/test.fitModels.R
monocle/tests/testthat/test.genSmoothCurves.R
monocle/tests/testthat/test.orderCells.R
monocle/tests/testthat/test.reduceDimension.R
monocle/tests/testthat/test.relative2abs.R
monocle/tests/testthat/test.scale_pseudotime.R
monocle/vignettes
monocle/vignettes/bifurcation_heatmap
monocle/vignettes/framed.sty
monocle/vignettes/monocle-concordance.tex
monocle/vignettes/monocle-vignette.Rnw
monocle/vignettes/monocle_alg.bib
monocle/vignettes/whbiocvignette.sty