Man pages for LieberInstitute/spatialLIBD
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
| 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 with ComplexHeatmap |
| 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_stat_cor | Layer modeling correlation of statistics |
| layer_stat_cor_plot | Visualize the correlation of layer modeling t-statistics with... |
| 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 |
