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

## Documentation for package ‘monocle3’ version 1.4.26

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O P R S T

## -- A --

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.

## -- B --

bpcells_prcomp_irlba | Principal Components Analysis on BPCells IterableMatrix

## -- C --

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.
convert_counts_matrix | Convert the counts matrix class in the given CDS.
counts_row_order | Generic to access cds row order BPCells counts matrix.
counts_row_order-method | Method to access cds row order BPCells counts matrix

## -- D --

detect_genes | Detects genes above minimum threshold.

## -- E --

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

## -- F --

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.

## -- G --

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

## -- I --

identity_table | Report matrix and model identity information.

## -- L --

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.

## -- M --

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.

## -- N --

new_cell_data_set | Create a new cell_data_set object.
normalized_counts | Return a size-factor normalized and (optionally) log-transformed expression matrix

## -- O --

order_cells | Orders cells according to pseudotime.

## -- P --

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_cells_per_sample_and_perturbation | Make a boxplot of the number of cells per sample, with each perturbation as a separate box. Optionally facet by a second value.
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_hybrid | Plot expression for one or more genes as a hybrid histogram-interval with a Sina plot overlay.
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_mito_umi_per_cell | Plot a histogram of the percentage of UMIs mapping to mitochondria for each cell.
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
plot_umi_per_cell | Plot a histogram of the number of UMIs per cell with an optional vertical line showing the cutoff for outliers.
plot_umi_per_cell_and_perturbation | Make a boxplot of the number of UMIs per cell, with each perturbation as a separate box. Optionally facet by a second value.
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

## -- R --

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

## -- S --

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_cds_row_order_matrix | Set the row-major order counts matrix in the assays slot of the CDS when the CDS has a BPCells counts matrix.
set_matrix_control | Verify and set the matrix_control parameter list.
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

## -- T --

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.