add10xVisiumAnalysis | Add analysis data from a 10x Genomics Visium experiment to a... |
add_images | Add non-standard images with the same dimensions as current... |
add_key | Create a unique spot identifier |
add_qc_metrics | Quality Control for Spatial Data |
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... |
multi_gene_z_score | Combine multiple continuous variables by averaging Z scores |
prep_stitched_data | Prepare stitched data for plotting |
read10xVisiumAnalysis | Load analysis data from a 10x Genomics Visium experiment |
read10xVisiumWrapper | Load data from a 10x Genomics Visium experiment and make it... |
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 |
spatialLIBD-package | spatialLIBD: spatialLIBD: an R/Bioconductor package to... |
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 |
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