Package index • MAGICR

Main Functions

Core MAGIC functionality

magic(): MAGIC: Markov Affinity-based Graph Imputation of Cells

magic_impute(): Perform MAGIC Imputation

magic_optimal_t(): Compute Optimal t

Diffusion Operator

Functions for building the diffusion operator

build_diffusion_operator(): Build Diffusion Operator (Pipeline)

magic_knn_graph(): Build k-Nearest Neighbors Graph

compute_alpha_kernel(): Compute Alpha-Decaying Kernel

magic_diffusion_operator(): Compute Diffusion Operator

kernel: Kernel and Graph Construction

diffusion: Diffusion Operations

Preprocessing

Data preprocessing utilities

library_size_normalize(): Library Size Normalization

sqrt_normalize(): Square Root Transformation

log_transform(): Log Transformation

preprocessing: Data Preprocessing

Analysis

Analysis and visualization functions

knnDREMI(): Compute kNN-DREMI

magic_knnDREMI(): Compute kNN-DREMI on MAGIC result

dremi: kNN-DREMI: Conditional Density Resampled Mutual Information

animate_magic(): Animate MAGIC Diffusion

plot_magic_genes(): Plot Gene-Gene Scatter

plot: MAGIC Plotting Functions

Utilities

Helper functions

procrustes_disparity(): Procrustes Disparity

matrix_power(): Matrix Power

plot_disparity(): Plot disparity curve

validate_data(): Validate input data

has_cpp_acceleration(): Check if C++ Acceleration is Available

magicr_config(): Get MAGICR Configuration

set_magicr_options(): Set MAGICR Options

matrix_is_equivalent(): Check Matrix Equivalence

utils: MAGICR Utility Functions

Seurat Integration

Functions for Seurat/SCE objects

seurat: Seurat Integration

GetMAGICData(): Extract MAGIC Results from Seurat Object

S3 Methods

Methods for magic objects

`[`(<magic>): Subset MAGIC result

Data

Example datasets

magic_testdata: Example Single-Cell Data for MAGICR