Package index • CytoSPACER

Main Functions

Core functions for running CytoSPACER analysis

run_cytospace(): Run CytoSPACE Analysis

run_cytospace_seurat(): Run CytoSPACER from Seurat Objects

main: Main CytoSPACER Analysis Functions

Data Input/Output

Functions for reading and writing data

read_cytospace_input(): Read CytoSPACER Input Files

read_visium_data(): Read Visium Data from SpaceRanger Output

write_cytospace_results(): Write CytoSPACER Results

data_io: Data Input/Output Functions for CytoSPACER

Preprocessing

Data preprocessing and normalization

normalize_expression(): Normalize Expression Data

downsample_expression(): Downsample Expression Matrix

rank_transform(): Rank Transform Expression Data

sample_cells() sample_cells_by_type(): Sample Single Cells by Cell Type Composition

estimate_fractions() estimate_cell_type_fractions(): Estimate Cell Type Fractions

estimate_cells_per_spot(): Estimate Cells per Spot

get_target_counts(): Compute Target Cell Counts

partition_indices(): Partition Indices

cell_sampling: Cell Sampling Functions for CytoSPACER

normalization: Data Normalization Functions for CytoSPACER

Core Algorithm

Linear assignment problem solver and cost matrix computation

solve_lap(): Solve Linear Assignment Problem

solve_lap_parallel(): Solve Multiple Assignment Problems in Parallel

compute_cost_matrix(): Compute Cost Matrix

compute_assignment_cost(): Compute Total Assignment Cost

add_noise_to_cost(): Add Noise to Cost Matrix

build_cost_matrix(): Build Cost Matrix for Multiple Cells per Spot

lap_solver: Linear Assignment Problem Solvers for CytoSPACER

cost_matrix: Cost Matrix Computation for CytoSPACER

Visualization

Plotting functions for results

plot_cytospace(): Plot CytoSPACER Results

plot_composition(): Plot Cell Type Composition

save_cytospace_plot(): Save CytoSPACER Plots

plotting: Visualization Functions for CytoSPACER

Seurat Integration

Functions for working with Seurat objects

extract_seurat_data(): Extract CytoSPACER Input from Seurat Object

extract_spatial_data(): Extract Spatial Data from Seurat Object

add_cytospace_to_seurat(): Add CytoSPACER Results to Seurat Object

seurat_integration: Seurat Integration Functions for CytoSPACER

Utilities

Internal utility functions

utils: Utility Functions for CytoSPACER

format_label(): Format Labels for Plotting

check_packages(): Check Package Availability

log_msg(): Create Log Message

safe_execute(): Execute with Error Handling

validate_path(): Validate File Path

get_system_info(): Get System Information

memory_usage(): Get Memory Usage

progress_msg(): Print Progress Message

set_seed_parallel(): Set Random Seed