Man pages for LieberInstitute/spatialLIBD
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

add10xVisiumAnalysisAdd analysis data from a 10x Genomics Visium experiment to a...
add_imagesAdd non-standard images with the same dimensions as current...
add_keyCreate a unique spot identifier
add_qc_metricsQuality Control for Spatial Data
annotate_registered_clustersAnnotated spatially-registered clusters
check_modeling_resultsCheck input modeling_results
check_sceCheck input sce
check_sce_layerCheck input sce_layer
check_speCheck input spe
cluster_exportExport a column with cluster results
cluster_importImport cluster results
enough_ramDetermine if you have enough RAM memory
fetch_dataDownload the Human DLPFC Visium data from LIBD
frame_limitsIdentify the image limits
gene_set_enrichmentEvaluate the enrichment for a list of gene sets
gene_set_enrichment_plotPlot the gene set enrichment results
geom_spatialA ggplot2 layer for visualizing the Visium histology
get_colorsObtain the colors for a set of cluster names
img_editEdit a background image
img_updateUpdate the image for one sample
img_update_allUpdate the images for all samples
layer_boxplotLayer-level (group-level) boxplots
layer_matrix_plotVisualize a matrix of values across human brain layers
layer_stat_corLayer modeling correlation of statistics
layer_stat_cor_plotVisualize the layer modeling correlation of statistics
libd_layer_colorsVector of LIBD layer colors
locate_imagesLocate image files
multi_gene_pcaCombine multiple continuous variables through PCA
multi_gene_sparsityCombine multiple continuous variables by proportion of...
multi_gene_z_scoreCombine multiple continuous variables by averaging Z scores
prep_stitched_dataPrepare stitched data for plotting
read10xVisiumAnalysisLoad analysis data from a 10x Genomics Visium experiment
read10xVisiumWrapperLoad data from a 10x Genomics Visium experiment and make it...
registration_block_corSpatial registration: block correlation
registration_modelSpatial registration: model
registration_pseudobulkSpatial registration: pseudobulk
registration_stats_anovaSpatial registration: compute ANOVA statistics
registration_stats_enrichmentSpatial registration: compute enrichment statistics
registration_stats_pairwiseSpatial registration: compute pairwise statistics
registration_wrapperSpatial registration: wrapper function
run_appRun the spatialLIBD Shiny Application
sce_to_speConvert a SCE object to a SPE one
sig_genes_extractExtract significant genes
sig_genes_extract_allExtract significant genes for all modeling results
sort_clustersSort clusters by frequency
spatialLIBD-packagespatialLIBD: spatialLIBD: an R/Bioconductor package to...
tstats_Human_DLPFC_snRNAseq_Nguyen_topLayerCell cluster t-statistics from Tran et al
vis_clusSample spatial cluster visualization
vis_clus_pSample spatial cluster visualization workhorse function
vis_geneSample spatial gene visualization
vis_gene_pSample spatial gene visualization workhorse function
vis_grid_clusSample spatial cluster visualization grid
vis_grid_geneSample spatial gene visualization grid
LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 a.m.