Man pages for cole-trapnell-lab/monocle3
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

aggregate_gene_expressionCreates a matrix with aggregated expression values for...
align_cdsAlign cells from different groups within a cds
calc_principal_graphFunction to automatically learn the structure of data by...
calculateLWFunction to calculate the neighbors list with spatial weights...
cell_data_setThe cell_data_set class
cell_data_set-methodsMethods for the cell_data_set class
choose_cellsChoose cells interactively to subset a cds
choose_graph_segmentsChoose cells along the path of a principal graph
clear_cds_slotsClear CDS slots
cluster_cellsCluster cells using Louvain/Leiden community detection
clustersGeneric to extract clusters from CDS object
clusters-cell_data_set-methodMethod to extract clusters from CDS object
coefficient_tableExtracts a table of coefficients from a tibble containing...
combine_cdsCombine a list of cell_data_set objects
compare_modelsCompares goodness of fit for two ways of fitting a set of...
detect_genesDetects genes above minimum threshold.
estimate_size_factorsFunction to calculate size factors for single-cell RNA-seq...
evaluate_fitsEvaluate the fits of model objects.
exprsGeneric to access cds count matrix
exprs-cell_data_set-methodMethod to access cds count matrix
fDataGeneric to access cds rowData table
fData-cell_data_set-methodGeneric to access cds rowData table
fData-setGeneric to set cds rowData table
fData-set-cell_data_set-methodMethod to set cds rowData table
find_gene_modulesCluster genes into modules that are co-expressed across...
find_nearest_vertexFinds the nearest principal graph node
fit_model_helperHelper function for model fitting
fit_modelsFits a model for each gene in a cell_data_set object.
generate_centersFunction to reproduce the behavior of eye function in matlab
generate_garnett_marker_fileGenerate a Garnett marker file from top_markers output.
get_citationsAccess citations for methods used during analysis.
get_genome_in_matrix_pathGet a genome from Cell Ranger output
graph_testTest genes for differential expression based on the low...
learn_graphLearn principal graph from the reduced dimension space using...
load_a549Build a cell_data_set from the data stored in inst/extdata...
load_cellranger_dataLoad data from the 10x Genomics Cell Ranger pipeline
load_mm_dataLoad data from matrix market format files.
load_mtx_dataLoad data from matrix market format
load_worm_embryoBuild a cell_data_set from the data stored in inst/extdata...
mc_es_applyMulticore apply-like function for cell_data_set
model_predictionsPredict output of fitted models and return as a matrix
my.aggregate.MatrixA function to aggregate columns within a matrix.
new_cell_data_setCreate a new cell_data_set object.
normalized_countsReturn a size-factor normalized and (optionally)...
order_cellsOrders cells according to pseudotime.
partitionsGeneric to extract partitions from CDS object
partitions-cell_data_set-methodMethod to extract partitions from CDS object
pDataGeneric to access cds colData table
pData-cell_data_set-methodMethod to access cds colData table
pData-setGeneric to set cds colData table
pData-set-cell_data_set-methodMethod to set cds colData table
plot_cellsPlots the cells along with their trajectories.
plot_cells_3dPlot a dataset and trajectory in 3 dimensions
plot_genes_by_groupCreate a dot plot to visualize the mean gene expression and...
plot_genes_in_pseudotimePlots expression for one or more genes as a function of...
plot_genes_violinPlot expression for one or more genes as a violin plot
plot_pc_variance_explainedPlots the percentage of variance explained by the each...
plot_percent_cells_positivePlots the number of cells expressing one or more genes above...
preprocess_cdsPreprocess a cds to prepare for trajectory inference
principal_graphGeneric to extract principal graph from CDS
principal_graph_auxGeneric to extract principal graph auxiliary information from...
principal_graph_aux-cell_data_set-methodMethod to extract principal graph auxiliary information from...
principal_graph_aux-setGeneric to set principal graph auxiliary information into CDS
principal_graph_aux-set-cell_data_set-methodMethod to set principal graph auxiliary information into CDS
principal_graph-cell_data_set-methodMethod to extract principal graph from CDS
principal_graph-setGeneric to set principal graph to CDS
principal_graph-set-cell_data_set-methodGeneric to set principal graph to CDS
pseudotimeGeneric to extract pseudotime from CDS object
pseudotime-cell_data_set-methodMethod to extract pseudotime from CDS object
reduce_dimensionCompute a projection of a cell_data_set object into a lower...
repmatfunction to reproduce the behavior of repmat function in...
size_factorsGet the size factors from a cds object.
size_factors-setSet the size factor values in the cell_data_set
soft_assignmentFunction to calculate the third term in the objective...
sparse_prcomp_irlbaPrincipal Components Analysis
top_markersIdentify the genes most specifically expressed in groups of...
cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.