Package: monocle 2.41.0

Cole Trapnell

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.

Authors:Cole Trapnell

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
monocle/json (API)

# Install 'monocle' in R:

install.packages('monocle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

spike_df - Spike-in transcripts data.

On BioConductor:monocle-2.41.0(bioc 3.24)monocle-2.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology sequencing rnaseq geneexpression differentialexpression infrastructure dataimport datarepresentation visualization clustering multiplecomparison qualitycontrol cpp

8.04 score 2 packages 1.8k scripts 60 mentions 61 exports 64 dependencies

Last updated from:733301c2e1. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	293
linux-devel-arm64	NOTE	297
linux-devel-x86_64	NOTE	391
source / vignettes	OK	448
linux-release-arm64	NOTE	293
linux-release-x86_64	NOTE	372
macos-release-arm64	NOTE	142
macos-release-x86_64	NOTE	280
macos-oldrel-arm64	NOTE	153
macos-oldrel-x86_64	NOTE	305
windows-devel	NOTE	225
windows-release	NOTE	240
windows-oldrel	NOTE	232
wasm-release	OK	610

Exports:addCellType BEAM branchTest buildBranchCellDataSet calABCs calculateMarkerSpecificity calILRs cellPairwiseDistances cellPairwiseDistances<-classifyCells clusterCells clusterGenes compareModels detectBifurcationPoint detectGenes differentialGeneTest dispersionTable estimate_t exportCDS fitModel genSmoothCurves get_classic_muscle_markers importCDS load_HSMM load_HSMM_markers load_lung markerDiffTable mcesApply minSpanningTree minSpanningTree<-newCellDataSet newCellTypeHierarchy orderCells plot_cell_clusters plot_cell_trajectory plot_clusters plot_complex_cell_trajectory plot_genes_branched_heatmap plot_genes_branched_pseudotime plot_genes_in_pseudotime plot_genes_jitter plot_genes_positive_cells plot_genes_violin plot_multiple_branches_heatmap plot_multiple_branches_pseudotime plot_ordering_genes plot_pc_variance_explained plot_pseudotime_heatmap plot_rho_delta plot_spanning_tree reducedDimA reducedDimA<-reducedDimK reducedDimS reducedDimW reduceDimension relative2abs responseMatrix selectTopMarkers setOrderingFilter vstExprs

Dependencies:BH Biobase BiocGenerics BiocManager biocViews bitops cli cluster combinat cpp11 DDRTree dplyr farver fastICA generics ggplot2 glue graph gridExtra gtable HSMMSingleCell igraph irlba isoband labeling lattice leidenbase lifecycle limma magrittr MASS Matrix matrixStats pheatmap pillar pkgconfig plyr proxy R6 RANN RBGL RColorBrewer Rcpp RcppEigen RCurl reshape2 rlang Rtsne RUnit S7 scales slam statmod stringi stringr tibble tidyselect utf8 vctrs VGAM viridis viridisLite withr XML

Monocle: Cell counting, differential expression, and trajectory analysis for single-cell RNA-Seq experiments

Rendered frommonocle-vignette.Rnwusingknitr::knitr

Last update: 2017-10-23
Started: 2014-07-10

Help page	Topics
Add a new cell type	addCellType
Branched expression analysis modeling (BEAM).	BEAM
Test for branch-dependent expression	branchTest
Build a CellDataSet that splits cells among two branches	buildBranchCellDataSet
Compute the area between curves (ABC) for branch-dependent genes	calABCs
Calibrate_per_cell_total_proposal	calibrate_per_cell_total_proposal
Calculate the Instantaneous Log Ratio between two branches	calILRs
The CellDataSet class	CellDataSet CellDataSet-class
Methods for the CellDataSet class	CellDataSet,ANY,ANY-method CellDataSet-methods estimateDispersions,CellDataSet-method estimateSizeFactors,CellDataSet-method sizeFactors,CellDataSet-method sizeFactors<-,CellDataSet,numeric-method
Get the matrix of pairwise distances between cells	cellPairwiseDistances
Sets the matrix containing distances between each pair of cells used by Monocle during cell ordering. Not intended to be called directly.	cellPairwiseDistances<-
The CellType class	CellType CellType-class
The CellTypeHierarchy class	CellTypeHierarchy CellTypeHierarchy-class
Cluster cells into a specified number of groups based on .	clusterCells
Clusters genes by pseudotime trend.	clusterGenes
Compare model fits	compareModels
Calculate divergence times for branch-dependent genes	detectBifurcationPoint
Detects genes above minimum threshold.	detectGenes
Helper function for parallel differential expression testing	diff_test_helper
Test genes for differential expression	differentialGeneTest
Retrieve a table of values specifying the mean-variance relationship	dispersionTable
Find the most commonly occuring relative expression value in each cell	estimate_t
Helper function to estimate dispersions	estimateDispersionsForCellDataSet
Function to calculate the size factor for the single-cell RNA-seq data @importFrom stats median	estimateSizeFactorsForMatrix
Export a monocle CellDataSet object to the Seurat single cell analysis toolkit.	exportCDS
Extract a linear ordering of cells from a PQ tree	extract_good_branched_ordering
Helper function for parallel VGAM fitting	fit_model_helper
Fits a model for each gene in a CellDataSet object.	fitModel
Fit smooth spline curves and return the residuals matrix	genSmoothCurveResiduals
Fit smooth spline curves and return the response matrix	genSmoothCurves
Return the names of classic muscle genes	get_classic_muscle_markers
Import a Seurat object and convert it to a monocle cds.	importCDS
Build a CellDataSet from the HSMMSingleCell package	load_HSMM
Return a CellDataSet of classic muscle genes.	load_HSMM_markers
Build a CellDataSet from the data stored in inst/extdata directory.	load_lung
Test genes for cell type-dependent expression	markerDiffTable
Multicore apply-like function for CellDataSet	mcesApply
Retrieves the minimum spanning tree generated by Monocle during cell ordering.	minSpanningTree
Set the minimum spanning tree generated by Monocle during cell ordering.	minSpanningTree<-
Creates a new CellDateSet object.	newCellDataSet
Classify cells according to a set of markers	calculateMarkerSpecificity classifyCells newCellTypeHierarchy
Return an ordering for a P node in the PQ tree	order_p_node
Orders cells according to pseudotime.	orderCells
Plots clusters of cells .	plot_cell_clusters
Plots the minimum spanning tree on cells.	plot_cell_trajectory
Plots kinetic clusters of genes.	plot_clusters
Not sure we're ready to release this one quite yet: Plot the branch genes in pseduotime with separate branch curves	plot_coexpression_matrix
Plots the minimum spanning tree on cells.	plot_complex_cell_trajectory
Create a heatmap to demonstrate the bifurcation of gene expression along two branchs @description returns a heatmap that shows changes in both lineages at the same time. It also requires that you choose a branch point to inspect. Columns are points in pseudotime, rows are genes, and the beginning of pseudotime is in the middle of the heatmap. As you read from the middle of the heatmap to the right, you are following one lineage through pseudotime. As you read left, the other. The genes are clustered hierarchically, so you can visualize modules of genes that have similar lineage-dependent expression patterns.	plot_genes_branched_heatmap
Plot the branch genes in pseduotime with separate branch curves.	plot_genes_branched_pseudotime
Plots expression for one or more genes as a function of pseudotime	plot_genes_in_pseudotime
Plots expression for one or more genes as a jittered, grouped points	plot_genes_jitter
Plots the number of cells expressing one or more genes as a barplot	plot_genes_positive_cells
Plots expression for one or more genes as a violin plot	plot_genes_violin
Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches	plot_multiple_branches_heatmap
Create a kinetic curves to demonstrate the bifurcation of gene expression along multiple branches	plot_multiple_branches_pseudotime
Plots genes by mean vs. dispersion, highlighting those selected for ordering	plot_ordering_genes
Plots the percentage of variance explained by the each component based on PCA from the normalized expression data using the same procedure used in reduceDimension function.	plot_pc_variance_explained
Plots a pseudotime-ordered, row-centered heatmap	plot_pseudotime_heatmap
Plots the decision map of density clusters .	plot_rho_delta
Plots the minimum spanning tree on cells. This function is deprecated.	plot_spanning_tree
Recursively builds and returns a PQ tree for the MST	pq_helper
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.	reducedDimA<-
Retrieves the the whitening matrix during independent component analysis.	reducedDimK
Sets the the whitening matrix during independent component analysis.	reducedDimK<-
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.	reducedDimS<-
Get the whitened expression values for a CellDataSet.	reducedDimW
Sets the whitened expression values for each cell prior to independent component analysis. Not intended to be called directly.	reducedDimW<-
Compute a projection of a CellDataSet object into a lower dimensional space	reduceDimension
Transform relative expression values into absolute transcript counts.	relative2abs
Response values	residualMatrix
Calculates response values.	responseMatrix
Select the most cell type specific markers	selectTopMarkers
Marks genes for clustering	setOrderingFilter
Spike-in transcripts data.	spike_df
Return a variance-stabilized matrix of expression values	vstExprs

Package: monocle 2.41.0

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

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