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MONOCLE 3

Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments. To use this package, you will need the R statistical computing environment (version 3.0 or later) and several packages available through Bioconductor and CRAN.

Details on how to install and use Monocle 3 are available on our website:

http://cole-trapnell-lab.github.io/monocle3/

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Version

Version

1.0.0

License

MIT + file LICENSE

Maintainer

Last Published

September 8th, 2021

Functions in monocle3 (1.0.0)

Choose cells interactively to subset a cds

clear_cds_slots

Clear CDS slots

Align cells from different groups within a cds

The cell_data_set class

aggregate_gene_expression

Creates a matrix with aggregated expression values for arbitrary groups of genes

cell_data_set-methods

Methods for the cell_data_set class

choose_graph_segments

Choose cells along the path of a principal graph

Cluster cells using Louvain/Leiden community detection

calc_principal_graph

Function to automatically learn the structure of data by either using L1-graph or the spanning-tree formulization

Function to calculate the neighbors list with spatial weights for the chosen coding scheme from a cell dataset object

fit_model_helper

Helper function for model fitting

Evaluate the fits of model objects.

estimate_size_factors

Function to calculate size factors for single-cell RNA-seq data

find_gene_modules

Cluster genes into modules that are co-expressed across cells.

pData<-,cell_data_set-method

Method to set cds colData table

Test genes for differential expression based on the low dimensional embedding and the principal graph

Learn principal graph from the reduced dimension space using reversed graph embedding

Generic to set cds colData table

plot_pc_variance_explained

Plots the percentage of variance explained by the each component based on PCA from the normalized expression data determined using preprocess_cds.

Fits a model for each gene in a cell_data_set object.

find_nearest_vertex

Finds the nearest principal graph node

Compares goodness of fit for two ways of fitting a set of genes' expression

Detects genes above minimum threshold.

exprs,cell_data_set-method

Method to access cds count matrix

generate_centers

Function to reproduce the behavior of eye function in matlab

Generic to access cds count matrix

coefficient_table

Extracts a table of coefficients from a tibble containing model objects

get_genome_in_matrix_path

Get a genome from Cell Ranger output

Combine a list of cell_data_set objects

Orders cells according to pseudotime.

Access citations for methods used during analysis.

pData,cell_data_set-method

Method to access cds colData table

plot_percent_cells_positive

Plots the number of cells expressing one or more genes above a given value as a barplot

fData,cell_data_set-method

Generic to access cds rowData table

fData<-,cell_data_set-method

Method to set cds rowData table

Preprocess a cds to prepare for trajectory inference

Load data from matrix market format

partitions,cell_data_set-method

Method to extract partitions from CDS object

Load data from matrix market format files.

Generic to access cds colData table

normalized_counts

Return a size-factor normalized and (optionally) log-transformed expression matrix

Plot a dataset and trajectory in 3 dimensions

new_cell_data_set

Create a new cell_data_set object.

generate_garnett_marker_file

Generate a Garnett marker file from top_markers output.

clusters,cell_data_set-method

Method to extract clusters from CDS object

principal_graph,cell_data_set-method

Method to extract principal graph from CDS

plot_genes_by_group

Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells

principal_graph_aux<-,cell_data_set-method

Method to set principal graph auxiliary information into CDS

reduce_dimension

Compute a projection of a cell_data_set object into a lower dimensional space with non-linear dimension reduction methods

Generic to extract pseudotime from CDS object

Generic to access cds rowData table

Plots the cells along with their trajectories.

principal_graph

Generic to extract principal graph from CDS

Multicore apply-like function for cell_data_set

load_worm_embryo

Build a cell_data_set from the data stored in inst/extdata directory.

Generic to extract partitions from CDS object

Generic to set cds rowData table

Generic to extract clusters from CDS object

principal_graph_aux<-

Generic to set principal graph auxiliary information into CDS

Build a cell_data_set from the data stored in inst/extdata directory.

load_cellranger_data

Load data from the 10x Genomics Cell Ranger pipeline

sparse_prcomp_irlba

Principal Components Analysis

pseudotime,cell_data_set-method

Method to extract pseudotime from CDS object

principal_graph_aux

Generic to extract principal graph auxiliary information from CDS

Identify the genes most specifically expressed in groups of cells

principal_graph_aux,cell_data_set-method

Method to extract principal graph auxiliary information from CDS

Set the size factor values in the cell_data_set

function to reproduce the behavior of repmat function in matlab to replicate and tile an matrix

model_predictions

Predict output of fitted models and return as a matrix

my.aggregate.Matrix

A function to aggregate columns within a matrix.

plot_genes_violin

Plot expression for one or more genes as a violin plot

principal_graph<-,cell_data_set-method

Generic to set principal graph to CDS

plot_genes_in_pseudotime

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

Get the size factors from a cds object.

principal_graph<-

Generic to set principal graph to CDS

soft_assignment

Function to calculate the third term in the objective function