spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data


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Documentation for package ‘spatialLIBD’ version 1.14.1

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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
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