Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

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Documentation for package ‘monocle3’ version 1.3.1

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aggregate_gene_expression Creates a matrix with aggregated expression values for arbitrary groups of genes
align_cds Align cells from different groups within a cds
align_transform Apply an alignment transform model to a cell_data_set.
calc_principal_graph Function to automatically learn the structure of data by either using L1-graph or the spanning-tree formulization
cell_data_set The cell_data_set class
cell_data_set-class The cell_data_set class
cell_data_set-methods Methods for the cell_data_set class
choose_cells Choose cells interactively to subset a cds
choose_graph_segments Choose cells along the path of a principal graph
clear_cds_slots Clear CDS slots
clusters Generic to extract clusters from CDS object
clusters-method Method to extract clusters from CDS object
cluster_cells Cluster cells using Louvain/Leiden community detection
coefficient_table Extract coefficient table from a fit_models result.
combine_cds Combine a list of cell_data_set objects
compare_models Compare goodness of fit of two models.
detect_genes Detects genes above minimum threshold.
estimate_size_factors Function to calculate size factors for single-cell RNA-seq data
evaluate_fits Evaluate fit of model objects.
exprs Generic to access cds count matrix
exprs-method Method to access cds count matrix
fData Generic to access cds rowData table
fData-method Method to access cds rowData table
fData<- Generic to set cds rowData table
fData<--method Method to set cds rowData table
find_gene_modules Cluster genes into modules that are co-expressed across cells.
fit_models Fits a model for each gene in a cell_data_set object.
fix_missing_cell_labels Replace NA cell column data values left after running transfer_cell_labels.
generate_centers Function to reproduce the behavior of eye function in matlab
generate_garnett_marker_file Generate a Garnett marker file from top_markers output.
get_citations Access citations for methods used during analysis.
get_genome_in_matrix_path Get a genome from Cell Ranger output
graph_test Test genes for differential expression based on the low dimensional embedding and the principal graph
identity_table Report matrix and model identity information.
learn_graph Learn principal graph from the reduced dimension space using reversed graph embedding
load_a549 Build a small cell_data_set.
load_cellranger_data Load data from the 10x Genomics Cell Ranger pipeline
load_mm_data Load data from matrix market format files.
load_monocle_objects Load a full Monocle3 cell_data_set.
load_mtx_data Load data from matrix market format
load_transform_models Load transform models into a cell_data_set.
load_worm_embryo Build a cell_data_set from C. elegans embryo data.
load_worm_l2 Build a cell_data_set from C. elegans L2 data.
make_cds_nn_index Make and store a nearest neighbor index in the cell_data_set.
make_nn_index Make a nearest neighbor index.
mc_es_apply Multicore apply-like function for cell_data_set
model_predictions Predict values of new data using fit_models model.
new_cell_data_set Create a new cell_data_set object.
normalized_counts Return a size-factor normalized and (optionally) log-transformed expression matrix
order_cells Orders cells according to pseudotime.
partitions Generic to extract partitions from CDS object
partitions-method Method to extract partitions from CDS object
pData Generic to access cds colData table
pData-method Method to access cds colData table
pData<- Generic to set cds colData table
pData<--method Method to set cds colData table
plot_cells Plots the cells along with their trajectories.
plot_cells_3d Plot a dataset and trajectory in 3 dimensions
plot_genes_by_group Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells
plot_genes_in_pseudotime Plots expression for one or more genes as a function of pseudotime
plot_genes_violin Plot expression for one or more genes as a violin plot
plot_pc_variance_explained Plots the fraction of variance explained by the each component based on PCA from the normalized expression data determined using preprocess_cds. This is the fraction of the component variance relative to the variance of the components retained in the PCA; not the total variance.
plot_percent_cells_positive Plots the number of cells expressing one or more genes above a given value as a barplot
preprocess_cds Preprocess a cds to prepare for trajectory inference
preprocess_transform Apply a preprocess transform model to a cell_data_set.
principal_graph Generic to extract principal graph from CDS
principal_graph-method Method to extract principal graph from CDS
principal_graph<- Generic to set principal graph to CDS
principal_graph<--method Generic to set principal graph to CDS
principal_graph_aux Generic to extract principal graph auxiliary information from CDS
principal_graph_aux-method Method to extract principal graph auxiliary information from CDS
principal_graph_aux<- Generic to set principal graph auxiliary information into CDS
principal_graph_aux<--method Method to set principal graph auxiliary information into CDS
pseudotime Generic to extract pseudotime from CDS object
pseudotime-method Method to extract pseudotime from CDS object
reduce_dimension Compute a projection of a cell_data_set object into a lower dimensional space with non-linear dimension reduction methods
reduce_dimension_transform Apply a reduce_dimension transform model to a cell_data_set.
repmat function to reproduce the behavior of repmat function in matlab to replicate and tile an matrix
save_monocle_objects Save a Monocle3 full cell_data_set.
save_transform_models Save cell_data_set transform models.
search_cds_nn_index Search a nearest neighbor index that is stored in the cds.
search_nn_index Search a nearest neighbor index.
search_nn_matrix Search a subject matrix for nearest neighbors to a query_matrix.
set_cds_nn_index Set a nearest neighor index in the cell_data_set.
set_nn_control Verify and set nearest neighbor parameter list.
size_factors Get the size factors from a cds object.
size_factors<- Set the size factor values in the cell_data_set
soft_assignment Function to calculate the third term in the objective function
sparse_prcomp_irlba Principal Components Analysis
top_markers Identify the genes most specifically expressed in groups of cells
transfer_cell_labels Transfer cell column data from a reference to a query cell_data_set.