All functions

add10xVisiumAnalysis()

Add analysis data from a 10x Genomics Visium experiment to a SPE object

add_images()

Add non-standard images with the same dimensions as current ones

add_key()

Create a unique spot identifier

annotate_registered_clusters()

Annotated spatially-registered clusters

check_modeling_results()

Check input modeling_results

check_sce()

Check input sce

check_sce_layer()

Check input sce_layer

check_spe()

Check input spe

cluster_export()

Export a column with cluster results

cluster_import()

Import cluster results

enough_ram()

Determine if you have enough RAM memory

fetch_data()

Download the Human DLPFC Visium data from LIBD

frame_limits()

Identify the image limits

gene_set_enrichment()

Evaluate the enrichment for a list of gene sets

gene_set_enrichment_plot()

Plot the gene set enrichment results

geom_spatial()

A ggplot2 layer for visualizing the Visium histology

get_colors()

Obtain the colors for a set of cluster names

img_edit()

Edit a background image

img_update()

Update the image for one sample

img_update_all()

Update the images for all samples

layer_boxplot()

Layer-level (group-level) boxplots

layer_matrix_plot()

Visualize a matrix of values across human brain layers

layer_stat_cor()

Layer modeling correlation of statistics

layer_stat_cor_plot()

Visualize the layer modeling correlation of statistics

libd_layer_colors

Vector of LIBD layer colors

locate_images()

Locate image files

multi_gene_pca()

Combine multiple continuous variables through PCA

multi_gene_sparsity()

Combine multiple continuous variables by proportion of positive values

multi_gene_z_score()

Combine multiple continuous variables by averaging Z scores

read10xVisiumAnalysis()

Load analysis data from a 10x Genomics Visium experiment

read10xVisiumWrapper()

Load data from a 10x Genomics Visium experiment and make it spatialLIBD-ready

registration_block_cor()

Spatial registration: block correlation

registration_model()

Spatial registration: model

registration_pseudobulk()

Spatial registration: pseudobulk

registration_stats_anova()

Spatial registration: compute ANOVA statistics

registration_stats_enrichment()

Spatial registration: compute enrichment statistics

registration_stats_pairwise()

Spatial registration: compute pairwise statistics

registration_wrapper()

Spatial registration: wrapper function

run_app()

Run the spatialLIBD Shiny Application

sce_to_spe()

Convert a SCE object to a SPE one

sig_genes_extract()

Extract significant genes

sig_genes_extract_all()

Extract significant genes for all modeling results

sort_clusters()

Sort clusters by frequency

tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer

Cell cluster t-statistics from Tran et al

vis_clus()

Sample spatial cluster visualization

vis_clus_p()

Sample spatial cluster visualization workhorse function

vis_gene()

Sample spatial gene visualization

vis_gene_p()

Sample spatial gene visualization workhorse function

vis_grid_clus()

Sample spatial cluster visualization grid

vis_grid_gene()

Sample spatial gene visualization grid