Package index • CellOracleR

Core Classes

Main R6 classes for CellOracleR analysis

Oracle: Oracle Class for In Silico Gene Perturbation Analysis

Links: Links Class for Network Analysis

Net: Net Class for GRN Inference

TFinfo: TFinfo Class for Motif Analysis

print(<Oracle>): Print method for Oracle

print(<Links>): Print method for Links

print(<Net>): Print method for Net

print(<TFinfo>): Print method for TFinfo

coef_to_links(): Create links data frame from GRN coefficients

Oracle Operations

Functions for creating and manipulating Oracle objects

create_oracle(): Create Oracle object from Seurat

load_oracle(): Load Oracle object from file

save_oracle(): Save Oracle object

simulate_shift(): Simulate gene perturbation shift

simulation_summary(): Summary of simulation results

GRN Inference

Gene regulatory network inference functions

fit_grn(): Fit GRN for perturbation simulation

fit_grn_coef_matrix(): Fit GRN coefficient matrix

fit_grn_bagging(): Fit GRN with bagging

get_links(): Get Links object for network analysis

coef_to_links(): Create links data frame from GRN coefficients

Network Analysis

Network analysis and characterization

filter_links(): Filter links by threshold

get_network_score(): Calculate network scores

get_network_entropy(): Calculate network entropy

identify_hubs(): Identify hub genes

find_network_motifs(): Find network motifs

compare_networks(): Compare networks between clusters

shortest_paths(): Calculate shortest paths between genes

export_network(): Export network to various formats

network_summary(): Calculate network statistics summary

Trajectory Analysis

Cell trajectory and fate prediction

markov_simulate(): Markov simulation of cell trajectories

summarize_trajectories(): Summarize Markov simulation trajectories

compute_pseudotime(): Compute pseudotime based on transition probability

compute_fate_probability(): Compute fate probability to terminal states

Motif Analysis

TF binding motif analysis

create_tfinfo(): Create TFinfo object from peak data

scan_motifs(): Scan peaks for TF motifs

load_tfinfo(): Load TFinfo object from file

save_tfinfo(): Save TFinfo object

create_base_grn(): Create base GRN from scATAC-seq data

load_base_grn(): Load pre-built base GRN

get_base_grn_from_cicero(): Get base GRN from Cicero/ATAC data

annotate_peaks(): Annotate peaks with nearby genes

extract_peaks_from_signac(): Process ATAC-seq peaks from Signac

Visualization

Plotting functions

visualization: Visualization Functions

plot_cluster(): Plot cells by cluster

plot_simulation_flow(): Plot perturbation simulation vector field

plot_quiver(): Plot quiver (cell-level velocity arrows)

plot_gene_expression(): Plot gene expression on embedding

plot_pseudotime(): Plot pseudotime on embedding

plot_network_graph(): Plot GRN as network graph

plot_degree_distribution(): Plot degree distribution

plot_scores_as_rank(): Plot network scores as ranked bar plot

plot_score_comparison(): Compare network scores between clusters

plot_simulation_combined(): Create combined simulation plot

Utilities

Helper functions

extract_expression(): Extract expression matrix from Seurat object

get_embedding(): Get embedding from Seurat object

setup_parallel(): Setup parallel backend

create_perturb_condition(): Create perturbation condition

get_perturb_value(): Get perturbation values from expression data