Package: SPIAT 1.7.1

Yuzhou Feng

SPIAT: Spatial Image Analysis of Tissues

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Authors:Anna Trigos [aut], Yuzhou Feng [aut, cre], Tianpei Yang [aut], Mabel Li [aut], John Zhu [aut], Volkan Ozcoban [aut], Maria Doyle [aut]

SPIAT_1.7.1.tar.gz
SPIAT_1.7.1.zip(r-4.5)SPIAT_1.7.1.zip(r-4.4)SPIAT_1.7.1.zip(r-4.3)
SPIAT_1.7.1.tgz(r-4.4-any)SPIAT_1.7.1.tgz(r-4.3-any)
SPIAT_1.7.1.tar.gz(r-4.5-noble)SPIAT_1.7.1.tar.gz(r-4.4-noble)
SPIAT_1.7.1.tgz(r-4.4-emscripten)SPIAT_1.7.1.tgz(r-4.3-emscripten)
SPIAT.pdf |SPIAT.html✨
SPIAT/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/trigosteam/spiat/issues

On BioConductor:SPIAT-1.7.0(bioc 3.20)SPIAT-1.6.0(bioc 3.19)

bioconductor-package

52 exports 1.64 score 110 dependencies

Last updated 14 days agofrom:77e929b251

Exports:AUC_of_cross_functionaverage_marker_intensity_within_radiusaverage_minimum_distanceaverage_nearest_neighbor_indexaverage_percentage_of_cells_within_radiuscalculate_cell_proportionscalculate_cross_functionscalculate_distance_to_margincalculate_entropycalculate_minimum_distances_between_celltypescalculate_pairwise_distances_between_celltypescalculate_percentage_of_gridscalculate_proportions_of_cells_in_structurecalculate_spatial_autocorrelationcalculate_summary_distances_between_celltypescalculate_summary_distances_of_cells_to_borderscomposition_of_neighborhoodscompute_gradientcrossing_of_crossKdefine_celltypesdefine_structuredimensionality_reduction_plotentropy_gradient_aggregatedformat_cellprofiler_to_speformat_codex_to_speformat_colData_to_speformat_halo_to_speformat_image_to_speformat_inform_to_speformat_spe_to_pppgrid_metricsidentify_bordering_cellsidentify_neighborhoodsimage_splittermarker_intensity_boxplotmarker_prediction_plotmarker_surface_plotmarker_surface_plot_stackmeasure_association_to_cell_propertiesmixing_score_summarynumber_of_cells_within_radiusplot_average_intensityplot_cell_categoriesplot_cell_distances_violinplot_cell_marker_levelsplot_cell_percentagesplot_composition_heatmapplot_distance_heatmapplot_marker_level_heatmappredict_phenotypesR_BCselect_celltypes

Dependencies:abindapclusteraskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicolorspacecowplotcpp11crayoncurlDBIdbplyrdbscanDelayedArraydeldirdittoSeqdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesgluegoftestgridExtragtablegtoolshmshttrIRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemmandmunsellnlmeopensslpheatmappillarpkgconfigplogrplyrpolyclippracmaprettyunitsprogresspurrrR6RANNrasterRColorBrewerRcppreshape2rjsonrlangRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentspSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrSummarizedExperimentsystensorterratibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectorzlibbioc