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

aggregate_gene_expression | Creates a matrix with aggregated expression values for... |

align_cds | Align cells from different groups within a cds |

calc_principal_graph | Function to automatically learn the structure of data by... |

calculateLW | Function to calculate the neighbors list with spatial weights... |

cell_data_set | 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 |

cluster_cells | Cluster cells using Louvain/Leiden community detection |

clusters | Generic to extract clusters from CDS object |

clusters-cell_data_set-method | Method to extract clusters from CDS object |

coefficient_table | Extracts a table of coefficients from a tibble containing... |

combine_cds | Combine a list of cell_data_set objects |

compare_models | Compares goodness of fit for two ways of fitting a set of... |

detect_genes | Detects genes above minimum threshold. |

estimate_size_factors | Function to calculate size factors for single-cell RNA-seq... |

evaluate_fits | Evaluate the fits of model objects. |

exprs | Generic to access cds count matrix |

exprs-cell_data_set-method | Method to access cds count matrix |

fData | Generic to access cds rowData table |

fData-cell_data_set-method | Generic to access cds rowData table |

fData-set | Generic to set cds rowData table |

fData-set-cell_data_set-method | Method to set cds rowData table |

find_gene_modules | Cluster genes into modules that are co-expressed across... |

find_nearest_vertex | Finds the nearest principal graph node |

fit_model_helper | Helper function for model fitting |

fit_models | Fits a model for each gene in a cell_data_set object. |

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... |

learn_graph | Learn principal graph from the reduced dimension space using... |

load_a549 | Build a cell_data_set from the data stored in inst/extdata... |

load_cellranger_data | Load data from the 10x Genomics Cell Ranger pipeline |

load_mm_data | Load data from matrix market format files. |

load_mtx_data | Load data from matrix market format |

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

mc_es_apply | Multicore apply-like function for cell_data_set |

model_predictions | Predict output of fitted models and return as a matrix |

my.aggregate.Matrix | A function to aggregate columns within a matrix. |

new_cell_data_set | Create a new cell_data_set object. |

normalized_counts | Return a size-factor normalized and (optionally)... |

order_cells | Orders cells according to pseudotime. |

partitions | Generic to extract partitions from CDS object |

partitions-cell_data_set-method | Method to extract partitions from CDS object |

pData | Generic to access cds colData table |

pData-cell_data_set-method | Method to access cds colData table |

pData-set | Generic to set cds colData table |

pData-set-cell_data_set-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... |

plot_genes_in_pseudotime | Plots expression for one or more genes as a function of... |

plot_genes_violin | Plot expression for one or more genes as a violin plot |

plot_pc_variance_explained | Plots the percentage of variance explained by the each... |

plot_percent_cells_positive | Plots the number of cells expressing one or more genes above... |

preprocess_cds | Preprocess a cds to prepare for trajectory inference |

principal_graph | Generic to extract principal graph from CDS |

principal_graph_aux | Generic to extract principal graph auxiliary information from... |

principal_graph_aux-cell_data_set-method | Method to extract principal graph auxiliary information from... |

principal_graph_aux-set | Generic to set principal graph auxiliary information into CDS |

principal_graph_aux-set-cell_data_set-method | Method to set principal graph auxiliary information into CDS |

principal_graph-cell_data_set-method | Method to extract principal graph from CDS |

principal_graph-set | Generic to set principal graph to CDS |

principal_graph-set-cell_data_set-method | Generic to set principal graph to CDS |

pseudotime | Generic to extract pseudotime from CDS object |

pseudotime-cell_data_set-method | Method to extract pseudotime from CDS object |

reduce_dimension | Compute a projection of a cell_data_set object into a lower... |

repmat | function to reproduce the behavior of repmat function in... |

size_factors | Get the size factors from a cds object. |

size_factors-set | Set the size factor values in the cell_data_set |

soft_assignment | Function to calculate the third term in the objective... |

sparse_prcomp_irlba | Principal Components Analysis |

top_markers | Identify the genes most specifically expressed in groups of... |

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