Package index • spacedeconv

Setup

set_cibersort_binary(): Register the Path to the CIBERSORT Script

set_cibersort_mat(): Register the Path to the CIBERSORT Signature Matrix

Preprocessing

subsetSCE(): Subset a SingleCellExperiment by Cell Type

subsetSPE(): Subset a SpatialExperiment by Spatial Coordinates

Main Workflow

deconvolution_methods: Supported Deconvolution Methods

preprocess(): Preprocess Single Cell and Spatial Data for spacedeconv

normalize(): Normalize Expression Data in SCE/SPE Objects

build_model(): Build a Reference Signature

deconvolute(): Deconvolution with spacedeconv

build_and_deconvolute(): Build Model and Deconvolute in One Step

available_results(): List Available Deconvolution Results in a SpatialExperiment

Custom access to methods

build_model_card(): No Signature for CARD

build_model_cell2location(): Build a cell2location Model

build_model_dot(): No Signature for DOT

build_model_immunedeconv(): No Signature for Immunedeconv

build_model_rctd(): No Signature for RCTD

build_model_spatial_dwls(): Build a SpatialDWLS Signature

build_model_spotlight(): Build a SPOTlight Model

deconvolute_card(): Deconvolute with CARD

deconvolute_cell2location(): Deconvolute with cell2location

deconvolute_dot(): Deconvolute with DOT

deconvolute_immunedeconv(): Deconvolute with immunedeconv

deconvolute_immunedeconv_mouse(): Deconvolute with immunedeconv (mouse)

deconvolute_rctd(): Deconvolute with RCTD

deconvolute_spatial_dwls(): Deconvolute with SpatialDWLS

deconvolute_spotlight(): Deconvolute with SPOTlight

Visualization

plot_gene(): Plot Gene Expression

plot_spatial(): Plot Spatial Results

plot_celltype(): Plot Cell Types (Deprecated)

plot_umi_count(): Plot UMI Counts

plot_ndetected_genes(): Plot Detected Genes per Spot

plot_most_abundant(): Plot Most Abundant Cell Type per Spot

plot_comparison(): Plot Cell Type Comparison

plot_scatter(): Compare Two Result Columns with a Scatterplot

plot_overview(): Plot Overview of a SpatialExperiment

Sample Data

single_cell_data_1: Example single-cell dataset 1 (Wu et al.)

single_cell_data_2: Example single-cell dataset 2 (Wu et al.)

single_cell_data_3: Example single-cell dataset 3 (Wu et al.)

single_cell_data_4: Example single-cell dataset 4 (Wu et al.)

spatial_data_1: Example spatial dataset 1 (Wu et al.)

spatial_data_2: Example spatial dataset 2 (Wu et al.)

spatial_data_3: Example spatial dataset 3 (Wu et al.)

spatial_data_4: Example spatial dataset 4 (Wu et al.)

Utils

aggregate_results(): Aggregate Deconvolution Results

annotate_spots(): Annotate Specific Spots in a SpatialExperiment

addCustomAnnotation(): Add a Custom Annotation Column

cluster(): Cluster SpatialExperiment Results

get_cluster_features(): Get Cluster Features

print_info(): Print Dataset Summary

filter_sample_id(): Filter by Sample ID

compare_signatures(): Compare Signatures

convert_human_to_mouse(): Map Human to Mouse Gene Symbols

convert_mouse_to_human(): Map Mouse to Human Gene Symbols

spatialcorr(): Create a Correlation Plot

get_lr(): Compute Ligand-Receptor Scores per Spot

gene_set_score(): Calculate Gene Set Score

scale_cell_counts(): Scale Relative Cell Fractions to Absolute Counts

corr_expr(): Correlation Heatmap of Signature Matrix

DecoupleR

get_decoupleR_reference(): Fetch decoupleR Reference Networks

compute_activities(): Compute Pathway and Transcription Factor Activities with decoupleR