| GeomPointFixed |
Man page
|
| GeomSegmentFixed |
Man page
|
| GeomTextFixed |
Man page
|
| GroupAnnotation |
Man page
|
| GroupAnnotation-class |
Man page
|
| HistoImage |
Man page
|
| HistoImage-class |
Man page
|
| HistoImaging |
Man page
|
| HistoImaging-class |
Man page
|
| HistologyImage |
Man page
|
| HistologyImage-class |
Man page
|
| HistologyImaging |
Man page
|
| HistologyImaging-class |
Man page
|
| ImageAnnotation |
Man page
|
| ImageAnnotation-class |
Man page
|
| MERFISH |
Man page
|
| MolecularAssay |
Man page
|
| MolecularAssay-class |
Man page
|
| NumericAnnotation |
Man page
|
| NumericAnnotation-class |
Man page
|
| SDEGS |
Man page
|
| SDEGS-class |
Man page
|
| SPATA2 |
Man page
|
| SPATA2-class |
Man page
|
| SlideSeqV1 |
Man page
|
| SpatialAnnotation |
Man page
|
| SpatialAnnotation-class |
Man page
|
| SpatialAnnotationScreening |
Man page
|
| SpatialAnnotationScreening-class |
Man page
|
| SpatialData |
Man page
|
| SpatialData-class |
Man page
|
| SpatialGradientScreening |
Man page
|
| SpatialGradientScreening-class |
Man page
|
| SpatialMethod |
Man page
|
| SpatialMethod-class |
Man page
|
| SpatialTrajectory |
Man page
|
| SpatialTrajectory-class |
Man page
|
| SpatialTrajectoryScreening |
Man page
|
| SpatialTrajectoryScreening-class |
Man page
|
| Trajectory |
Man page
|
| Trajectory-class |
Man page
|
| VisiumHD |
Man page
|
| VisiumLarge |
Man page
|
| VisiumSmall |
Man page
|
| Xenium |
Man page
|
| activateAssay |
Man page
Source code
|
| activateGrouping |
Man page
Source code
|
| activateImage |
Man page
|
| activateImage,SPATA2-method |
Man page
|
| activateImage,SpatialData-method |
Man page
|
| activateImageInt |
Man page
|
| activateImageInt,SPATA2-method |
Man page
|
| activateImageInt,SpatialData-method |
Man page
|
| activateMatrix |
Man page
Source code
|
| activeAssay |
Man page
Source code
|
| activeGrouping |
Man page
Source code
|
| activeImage |
Man page
|
| activeImage,SPATA2-method |
Man page
|
| activeImage,SpatialData-method |
Man page
|
| activeMatrix |
Man page
Source code
|
| addAutoencoderSetUp |
Man page
|
| addExpressionMatrix |
Man page
Source code
|
| addFeatures |
Man page
|
| addGeneSet |
Man page
|
| addGeneSetsInteractive |
Source code
|
| addHistoImage |
Man page
|
| addHistoImage,SpatialData-method |
Man page
|
| addImageAnnotation |
Man page
Source code
|
| addInnerBorder |
Man page
|
| addInnerBorder,SPATA2-method |
Man page
|
| addInnerBorder,SpatialAnnotation-method |
Man page
|
| addMetaDataMol |
Man page
Source code
|
| addMetaDataObs |
Man page
Source code
|
| addMetaboliteSet |
Man page
|
| addMoleculeCoordinates |
Man page
Source code
|
| addPointsBase |
Man page
|
| addPolygonBase |
Man page
|
| addProcessedMatrix |
Man page
|
| addProteinSet |
Man page
|
| addSegmentationVariable |
Man page
|
| addSignature |
Man page
|
| addSpCorCluster |
Man page
Source code
|
| addSpatialAnnotation |
Man page
|
| addSpatialAnnotation,SPATA2-method |
Man page
|
| addSpatialAnnotation,SpatialData-method |
Man page
|
| addSpatialTrajectory |
Man page
|
| addTissueOutlineBase |
Man page
|
| addTissueOutlineBase,HistoImage-method |
Man page
|
| addVarToCoords |
Man page
|
| addVarToCoords,SpatialData-method |
Man page
|
| add_benchmarking_variables |
Source code
|
| add_dbscan_variable |
Man page
|
| add_edge_variable |
Man page
|
| add_grid_variable |
Man page
Source code
|
| add_models |
Man page
|
| add_noise_to_model |
Man page
|
| add_tissue_section_variable |
Man page
|
| add_wh |
Man page
|
| add_xy |
Man page
|
| adjustDefaultInstructions |
Man page
Source code
|
| adjustGeneSetList |
Man page
Source code
|
| adjustGseaDf |
Source code
|
| affineNumInput |
Source code
|
| affineSliderInput |
Source code
|
| alignImage |
Man page
|
| alignImage,HistoImage-method |
Man page
|
| alignImage,SPATA2-method |
Man page
|
| alignImage,SpatialData-method |
Man page
|
| alignImageAuto |
Man page
|
| alignImageAuto,SpatialData-method |
Man page
|
| alignImageInteractive |
Man page
|
| alignImageInteractive,SPATA2-method |
Man page
|
| alignImageInteractive,SpatialData-method |
Man page
|
| align_grid_with_coordinates |
Source code
Source code
|
| allColorpalettes |
Man page
|
| allColorspectra |
Man page
|
| all_color_palettes |
Man page
|
| all_color_spectra |
Man page
|
| append_polygon_df |
Man page
Source code
|
| are_all_area_or_dist |
Man page
|
| are_all_dist |
Man page
|
| argument_dummy |
Man page
Source code
|
| arrange_as_polygon |
Man page
Source code
|
| arrange_by_outline_variable |
Source code
|
| asGiotto |
Man page
Source code
|
| asMolecularAssay |
Man page
|
| asMolecularAssay,Assay-method |
Man page
|
| asMolecularAssay,Assay5-method |
Man page
|
| asSPATA2 |
Man page
|
| asSPATA2,Seurat-method |
Man page
|
| asSPATA2,giotto-method |
Man page
|
| asSeurat |
Man page
Source code
|
| asSingleCellExperiment |
Man page
Source code
|
| asSpatialTrajectory |
Man page
Source code
|
| asSummarizedExperiment |
Man page
Source code
|
| as_SPATA2_dist |
Man page
Source code
|
| as_centimeter |
Man page
Source code
|
| as_centimeter2 |
Man page
Source code
|
| as_decimeter |
Man page
Source code
|
| as_decimeter2 |
Man page
Source code
|
| as_meter |
Man page
Source code
|
| as_meter2 |
Man page
Source code
|
| as_micrometer |
Man page
Source code
|
| as_micrometer2 |
Man page
Source code
|
| as_millimeter |
Man page
Source code
|
| as_millimeter2 |
Man page
Source code
|
| as_nanometer |
Man page
Source code
|
| as_nanometer2 |
Man page
Source code
|
| as_pixel |
Man page
Source code
|
| as_unit |
Man page
Source code
|
| assessAutoencoderOptions |
Man page
Source code
|
| attachUnit |
Man page
Source code
|
| average_genes |
Man page
Source code
|
| background_white |
Man page
Source code
|
| barcodesToSpatialAnnotation |
Man page
Source code
|
| binwidth_dummy |
Man page
Source code
|
| buffer_area |
Man page
|
| cds_dummy |
Man page
Source code
|
| centerSpatialAnnotation |
Man page
|
| centerSpatialAnnotation,SPATA2-method |
Man page
|
| centerSpatialAnnotation,SpatialData-method |
Man page
|
| centerTissueOutline |
Man page
|
| centerTissueOutline,HistoImage-method |
Man page
|
| center_polygon |
Source code
|
| checkShortcut |
Source code
|
| check_assign |
Man page
Source code
|
| check_availability |
Man page
Source code
|
| check_binwidth_n_bins |
Source code
|
| check_color_to |
Man page
Source code
|
| check_coordinate_variables |
Man page
Source code
|
| check_coords_df |
Man page
Source code
|
| check_cran_packages |
Source code
|
| check_dea_df |
Man page
Source code
|
| check_display |
Man page
Source code
|
| check_expand |
Source code
|
| check_expand_shiny |
Source code
|
| check_feature_df |
Man page
Source code
|
| check_features |
Man page
Source code
|
| check_gene_sets |
Man page
Source code
|
| check_genes |
Man page
Source code
|
| check_image_annotation_ids |
Source code
|
| check_image_annotation_tags |
Source code
|
| check_matrix_name |
Source code
|
| check_method |
Man page
Source code
|
| check_monocle_input |
Man page
Source code
|
| check_monocle_packages |
Man page
Source code
|
| check_new_variable_name |
Source code
|
| check_object |
Source code
|
| check_packages |
Source code
|
| check_paths |
Man page
Source code
|
| check_pattern |
Man page
Source code
|
| check_pt |
Man page
Source code
|
| check_sample |
Man page
Source code
|
| check_sas_input |
Source code
|
| check_saving |
Man page
Source code
|
| check_segment |
Man page
Source code
|
| check_smooth |
Man page
Source code
|
| check_spata_df |
Man page
Source code
|
| check_spatial_data |
Source code
|
| check_square_res |
Source code
|
| check_stdf |
Man page
Source code
|
| check_summarized_trajectory_df |
Man page
Source code
|
| check_to |
Man page
Source code
|
| check_trajectory |
Man page
Source code
|
| check_trajectory_binwidth |
Man page
Source code
|
| check_uniform_genes |
Man page
Source code
|
| check_variables |
Man page
Source code
|
| checkpoint |
Man page
Source code
|
| close_area_df |
Man page
Source code
|
| clrp |
Man page
Source code
|
| clrp_dummy |
Man page
Source code
|
| clusterSpCorResults |
Man page
Source code
|
| cnv_ref |
Man page
|
| cnv_regions_df |
Man page
|
| color_vector |
Man page
|
| complete_visium_coords_df |
Source code
|
| computeCaptureArea |
Man page
|
| computeCaptureArea,SPATA2-method |
Man page
|
| computeCaptureArea,SpatialData-method |
Man page
|
| computeChromosomalInstability |
Man page
Source code
|
| computeCnvByChrArm |
Man page
Source code
|
| computeCountPercentage |
Man page
Source code
|
| computeMetaFeatures |
Man page
Source code
|
| computePixelScaleFactor |
Man page
|
| computePixelScaleFactor,SPATA2-method |
Man page
|
| computePixelScaleFactor,SpatialData-method |
Man page
|
| compute_angle_between_two_points |
Man page
Source code
|
| compute_area |
Source code
|
| compute_avg_dp_distance |
Source code
|
| compute_avg_vertex_distance |
Source code
|
| compute_corr |
Source code
|
| compute_correction_factor_sas |
Source code
|
| compute_correction_factor_sts |
Source code
|
| compute_dist_screened |
Source code
|
| compute_distance |
Man page
Source code
|
| compute_expression_estimates |
Man page
Source code
|
| compute_img_scale_fct |
Man page
Source code
|
| compute_mae |
Source code
|
| compute_overlap_polygon |
Source code
|
| compute_overlap_st_polygon |
Source code
|
| compute_pairwise_distances |
Source code
|
| compute_relative_variation |
Source code
|
| compute_rho |
Source code
|
| compute_rmse |
Source code
|
| compute_tau |
Source code
|
| compute_total_variation |
Source code
|
| concept_active |
Man page
|
| concept_area_measure |
Man page
|
| concept_distance_measure |
Man page
|
| concept_images |
Man page
|
| concept_logfile |
Man page
|
| concept_molecular_modalities |
Man page
|
| concept_molecular_signatures |
Man page
|
| concept_observations |
Man page
|
| concept_scale_factors |
Man page
|
| concept_spatial_annotation |
Man page
|
| concept_spatial_trajectory |
Man page
|
| concept_tissue_outline |
Man page
|
| concept_variables |
Man page
|
| containsAssay |
Man page
Source code
|
| containsCCD |
Man page
|
| containsCCD,ANY-method |
Man page
|
| containsCNV |
Man page
Source code
|
| containsCaptureArea |
Man page
|
| containsCaptureArea,SPATA2-method |
Man page
|
| containsCaptureArea,SpatialData-method |
Man page
|
| containsCells |
Man page
|
| containsCells,ANY-method |
Man page
|
| containsHistoImages |
Man page
|
| containsHistoImages,SPATA2-method |
Man page
|
| containsHistoImages,SpatialData-method |
Man page
|
| containsHistologyImaging |
Man page
Source code
|
| containsImage |
Man page
|
| containsImage,ANY-method |
Man page
|
| containsImage,HistoImage-method |
Man page
|
| containsImage,SpatialAnnotation-method |
Man page
|
| containsInnerBorders |
Man page
|
| containsInnerBorders,SPATA2-method |
Man page
|
| containsInnerBorders,SpatialAnnotation-method |
Man page
|
| containsInnerBorders,data.frame-method |
Man page
|
| containsMethod |
Man page
|
| containsMethod,SPATA2-method |
Man page
|
| containsMethod,SpatialData-method |
Man page
|
| containsModality |
Man page
Source code
|
| containsMoleculeCoordinates |
Man page
Source code
|
| containsPixelContent |
Man page
|
| containsPixelContent,HistoImage-method |
Man page
|
| containsPixelContent,SpatialData-method |
Man page
|
| containsPseudoImage |
Man page
|
| containsPseudoImage,ANY-method |
Man page
|
| containsScaleFactor |
Man page
|
| containsScaleFactor,SPATA2-method |
Man page
|
| containsScaleFactor,SpatialData-method |
Man page
|
| containsSpatialAnnotations |
Man page
|
| containsSpatialAnnotations,SPATA2-method |
Man page
|
| containsSpatialAnnotations,SpatialData-method |
Man page
|
| containsSpatialData |
Man page
Source code
|
| containsSpatialOutliers |
Man page
Source code
|
| containsSpots |
Man page
|
| containsSpots,ANY-method |
Man page
|
| containsTissueOutline |
Man page
|
| containsTissueOutline,HistoImage-method |
Man page
|
| containsTissueOutline,SPATA2-method |
Man page
|
| containsTissueOutline,SpatialData-method |
Man page
|
| containsVersion |
Man page
Source code
|
| countImageAnnotationTags |
Man page
|
| createGroupAnnotations |
Man page
|
| createHistoImage |
Man page
|
| createImageAnnotations |
Man page
|
| createMolecularAssay |
Man page
|
| createNumericAnnotations |
Man page
|
| createSegmentation |
Man page
Source code
|
| createSpatialData |
Man page
|
| createSpatialDataMERFISH |
Man page
|
| createSpatialDataSlideSeqV1 |
Man page
|
| createSpatialDataVisium |
Man page
|
| createSpatialDataVisiumHD |
Man page
|
| createSpatialDataXenium |
Man page
|
| createSpatialMethod |
Man page
|
| createSpatialSegmentation |
Man page
Source code
|
| createSpatialTrajectories |
Man page
|
| createTrajectories |
Man page
Source code
|
| createTrajectoryManually |
Man page
Source code
|
| create_circle_polygon |
Source code
|
| create_encircling_add_on |
Source code
|
| create_image_annotations_ui |
Source code
|
| create_model_df |
Man page
Source code
|
| cropSpataObject |
Man page
|
| crop_image |
Man page
|
| currentSpata2Version |
Man page
|
| data_counts |
Man page
|
| data_counts-class |
Man page
|
| defaultGeomObs |
Man page
Source code
|
| default_instructions |
Man page
|
| default_instructions-class |
Man page
|
| deprecated |
Source code
|
| deprecatedArguments |
Source code
|
| deprecatedInfo |
Man page
Source code
|
| dim_red |
Man page
|
| dim_red-class |
Man page
|
| discardExpressionMatrix |
Source code
|
| discard_uniform_variables |
Source code
|
| dissolveGroups |
Man page
Source code
|
| distToEdge |
Man page
Source code
|
| downgrade |
Source code
|
| downloadFromPublication |
Man page
Source code
|
| downloadSpataObject |
Man page
|
| downloadSpataObjects |
Man page
|
| dropped_df_dummy |
Man page
Source code
|
| enhanceSpataObject |
Source code
|
| estimate_r2_for_sas_run |
Source code
|
| estimate_r2_for_sts_run |
Source code
|
| evaluate_model_fits |
Source code
|
| example_data |
Man page
|
| exchangeImage |
Man page
Source code
|
| expandSpatialAnnotation |
Man page
Source code
|
| expand_image_range |
Source code
|
| expand_image_side |
Source code
|
| export |
Man page
Source code
|
| extract_bin_dist_val |
Source code
|
| extract_row_col_vars_visiumHD |
Man page
Source code
|
| extract_unit |
Man page
Source code
|
| extract_value |
Man page
Source code
|
| extract_var_names |
Man page
Source code
|
| feedback_area_input |
Source code
|
| feedback_area_pixel_input |
Source code
|
| feedback_area_si_input |
Source code
|
| feedback_distance_input |
Source code
|
| feedback_expand_input |
Source code
|
| feedback_missing |
Source code
|
| feedback_percentage_input |
Source code
|
| feedback_pos |
Source code
|
| feedback_range_input |
Source code
|
| feedback_spatial_measure |
Source code
|
| filterDeaDf |
Man page
Source code
|
| filterSpataObject |
Man page
Source code
|
| filter_by_best |
Source code
|
| filter_by_model |
Source code
|
| filter_by_thresholds |
Source code
|
| findSDEGS |
Man page
Source code
|
| find_elbow_point |
Source code
|
| find_neighbors_visiumHD |
Man page
Source code
|
| find_path |
Man page
Source code
|
| flexible_call_dummy |
Man page
Source code
|
| flipAll |
Man page
Source code
|
| flipCaptureArea |
Man page
Source code
|
| flipCoordinates |
Man page
Source code
|
| flipCoords |
Man page
Source code
|
| flipCoordsDf |
Man page
Source code
|
| flipImage |
Man page
Source code
|
| flipSpatialAnnotations |
Man page
Source code
|
| flipSpatialTrajectories |
Man page
Source code
|
| flip_coords_df |
Man page
Source code
|
| gene_pos_df |
Man page
|
| gene_set_path |
Man page
Source code
|
| geom_point_fixed |
Man page
Source code
|
| geom_segment_fixed |
Man page
Source code
|
| geom_text_fixed |
Man page
Source code
|
| getActive |
Man page
|
| getActive,SPATA2-method |
Man page
|
| getActiveExpressionMatrixName |
Man page
Source code
|
| getActiveMatrixName |
Man page
Source code
|
| getAssay |
Man page
|
| getAssayModalities |
Man page
|
| getAssayNames |
Man page
|
| getAutoencoderAssessment |
Man page
Source code
|
| getAutoencoderSetUp |
Man page
Source code
|
| getBackgroundColor |
Man page
|
| getBackgroundColor,HistoImage-method |
Man page
|
| getBackgroundColor,SPATA2-method |
Man page
|
| getBackgroundColor,SpatialData-method |
Man page
|
| getBarcodeSpotDistance |
Man page
Source code
|
| getBarcodeSpotDistances |
Man page
|
| getBarcodes |
Man page
|
| getBarcodesInPolygon |
Man page
|
| getBarcodesInPolygonList |
Man page
|
| getCCD |
Man page
|
| getCCD,SPATA2-method |
Man page
|
| getCCD,SpatialData-method |
Man page
|
| getCaptureArea |
Man page
|
| getCaptureArea,SPATA2-method |
Man page
|
| getCaptureArea,SpatialData-method |
Man page
|
| getChrRegionsDf |
Man page
|
| getCnvFeatureNames |
Man page
|
| getCnvGenesDf |
Man page
|
| getCnvResults |
Man page
|
| getCoordsCenter |
Man page
|
| getCoordsDf |
Man page
|
| getCoordsDf,SPATA2-method |
Man page
|
| getCoordsDf,SpatialData-method |
Man page
|
| getCoordsDfSA |
Man page
|
| getCoordsDfST |
Man page
|
| getCoordsMtr |
Man page
|
| getCoordsRange |
Man page
|
| getCountMatrix |
Man page
|
| getCountMatrix,MolecularAssay-method |
Man page
|
| getCountMatrix,SPATA2-method |
Man page
|
| getDeaGenes |
Man page
|
| getDeaLfcName |
Man page
|
| getDeaResultsDf |
Man page
|
| getDefault |
Man page
|
| getDefaultGrouping |
Man page
Source code
|
| getDefaultInstructions |
Man page
|
| getDefaultUnit |
Man page
|
| getDimRedDf |
Man page
|
| getExpressionMatrix |
Man page
Source code
|
| getExpressionMatrixNames |
Man page
Source code
|
| getFeatureDf |
Man page
Source code
|
| getFeatureNames |
Man page
|
| getFromSeurat |
Man page
|
| getGeneDistDf |
Source code
|
| getGeneDistMtr |
Man page
Source code
|
| getGeneMetaData |
Man page
Source code
|
| getGeneMetaDf |
Man page
Source code
|
| getGenePosDf |
Man page
|
| getGeneSet |
Man page
|
| getGeneSetDf |
Man page
|
| getGeneSetList |
Man page
|
| getGeneSetOverview |
Man page
|
| getGeneSets |
Man page
|
| getGenes |
Man page
|
| getGridVisiumHD |
Man page
|
| getGroupNames |
Man page
|
| getGroupingOptions |
Man page
|
| getGseaDf |
Man page
|
| getGseaResults |
Man page
|
| getHistoImage |
Man page
|
| getHistoImage,SPATA2-method |
Man page
|
| getHistoImage,SpatialData-method |
Man page
|
| getHistoImageRef |
Man page
|
| getHistoImageRef,SPATA2-method |
Man page
|
| getHistoImageRef,SpatialData-method |
Man page
|
| getImage |
Man page
|
| getImage,HistoImage-method |
Man page
|
| getImage,SPATA2-method |
Man page
|
| getImage,SpatialData-method |
Man page
|
| getImageAnnotationAreaDf |
Man page
Source code
|
| getImageAnnotationCenter |
Man page
Source code
|
| getImageAnnotationIds |
Man page
Source code
|
| getImageAnnotationTags |
Man page
Source code
|
| getImageCenter |
Man page
|
| getImageCenter,HistoImage-method |
Man page
|
| getImageCenter,SPATA2-method |
Man page
|
| getImageCenter,SpatialData-method |
Man page
|
| getImageDf |
Man page
|
| getImageDf,HistoImage-method |
Man page
|
| getImageDf,Image-method |
Man page
|
| getImageDf,SPATA2-method |
Man page
|
| getImageDf,SpatialAnnotation-method |
Man page
|
| getImageDf,SpatialData-method |
Man page
|
| getImageDims |
Man page
|
| getImageDims,HistoImage-method |
Man page
|
| getImageDims,SPATA2-method |
Man page
|
| getImageDims,SpatialData-method |
Man page
|
| getImageDir |
Man page
|
| getImageDirDefault |
Man page
Source code
|
| getImageDirHighres |
Man page
Source code
|
| getImageDirLowres |
Man page
Source code
|
| getImageDirectories |
Man page
|
| getImageNames |
Man page
|
| getImageNames,SPATA2-method |
Man page
|
| getImageNames,SpatialData-method |
Man page
|
| getImageRange |
Man page
|
| getImageRange,HistoImage-method |
Man page
|
| getImageRange,SPATA2-method |
Man page
|
| getImageRange,SpatialData-method |
Man page
|
| getImageRaster |
Man page
|
| getImageRaster,HistoImage-method |
Man page
|
| getImageRaster,SPATA2-method |
Man page
|
| getImageRasterInfo |
Man page
|
| getImageSectionsByBarcode |
Man page
|
| getImageTransformations |
Man page
|
| getImageTransformations,HistoImage-method |
Man page
|
| getImageTransformations,SPATA2-method |
Man page
|
| getImageTransformations,SpatialData-method |
Man page
|
| getImgAnnArea |
Man page
Source code
|
| getImgAnnBorderDf |
Man page
Source code
|
| getImgAnnCenter |
Man page
Source code
|
| getImgAnnCenters |
Man page
Source code
|
| getImgAnnIds |
Man page
Source code
|
| getImgAnnOutlineDf |
Man page
Source code
|
| getImgAnnRange |
Man page
Source code
|
| getImgAnnTags |
Man page
Source code
|
| getLogfileDf |
Man page
|
| getMatrices |
Man page
|
| getMatrices,MolecularAssay-method |
Man page
|
| getMatrices,SPATA2-method |
Man page
|
| getMatrix |
Man page
|
| getMatrix,MolecularAssay-method |
Man page
|
| getMatrix,SPATA2-method |
Man page
|
| getMatrixNames |
Man page
|
| getMatrixNames,MolecularAssay-method |
Man page
|
| getMatrixNames,SPATA2-method |
Man page
|
| getMetaDf |
Man page
|
| getMetaNames |
Man page
|
| getMetaVarDf |
Man page
Source code
|
| getMetaboliteOverview |
Man page
|
| getMetaboliteSet |
Man page
|
| getMetaboliteSetList |
Man page
|
| getMetaboliteSets |
Man page
|
| getMetabolites |
Man page
|
| getMethodSpecifics |
Man page
|
| getModality |
Man page
|
| getModality,MolecularAssay-method |
Man page
|
| getModality,SPATA2-method |
Man page
|
| getMoleculeCoordinates |
Man page
Source code
|
| getMoleculeTypeList |
Man page
|
| getMolecules |
Man page
|
| getPatternNames |
Man page
Source code
|
| getPcaDf |
Man page
Source code
|
| getPcaMtr |
Man page
Source code
|
| getPixelDf |
Man page
|
| getPixelDf,HistoImage-method |
Man page
|
| getPixelDf,Image-method |
Man page
|
| getPixelDf,SPATA2-method |
Man page
|
| getPixelDf,SpatialData-method |
Man page
|
| getPixelScaleFactor |
Man page
|
| getPixelScaleFactor,HistoImage-method |
Man page
|
| getPixelScaleFactor,SPATA2-method |
Man page
|
| getPixelScaleFactor,SpatialData-method |
Man page
|
| getPlatform |
Man page
|
| getPlatform,SPATA2-method |
Man page
|
| getPlatform,SpatialData-method |
Man page
|
| getPointSize |
Source code
|
| getPrResults |
Man page
Source code
|
| getProcessedMatrix |
Man page
|
| getProcessedMatrix,MolecularAssay-method |
Man page
|
| getProcessedMatrix,SPATA2-method |
Man page
|
| getProcessedMatrixNames |
Man page
|
| getProcessedMatrixNames,MolecularAssay-method |
Man page
|
| getProcessedMatrixNames,SPATA2-method |
Man page
|
| getProjectionDf |
Man page
|
| getProteinSet |
Man page
|
| getProteinSetList |
Man page
|
| getProteinSetOverview |
Man page
|
| getProteinSets |
Man page
|
| getProteins |
Man page
|
| getResultsDf |
Man page
Source code
|
| getResultsVec |
Man page
Source code
|
| getSampleAreaSize |
Man page
Source code
|
| getSampleName |
Man page
|
| getSasDf |
Man page
|
| getScaleFactor |
Man page
|
| getScaleFactor,HistoImage-method |
Man page
|
| getScaleFactor,SPATA2-method |
Man page
|
| getScaleFactor,SpatialData-method |
Man page
|
| getSegmentationNames |
Man page
Source code
|
| getSgsResultsDf |
Man page
|
| getSgsResultsDf,SpatialGradientScreening-method |
Man page
|
| getSgsResultsVec |
Man page
|
| getSgsResultsVec,SpatialGradientScreening-method |
Man page
|
| getSignature |
Man page
|
| getSignatureList |
Man page
|
| getSignatureNames |
Man page
|
| getSignatureOverview |
Man page
|
| getSignatureTypeList |
Man page
|
| getSmrdResultsDf |
Man page
Source code
|
| getSpCorCluster |
Man page
Source code
|
| getSpCorClusterNames |
Man page
Source code
|
| getSpCorResults |
Man page
Source code
|
| getSparkxGeneDf |
Man page
|
| getSparkxGenes |
Man page
|
| getSparkxResults |
Man page
|
| getSpatAnnArea |
Man page
|
| getSpatAnnArea,SPATA2-method |
Man page
|
| getSpatAnnArea,SpatialData-method |
Man page
|
| getSpatAnnBarcodes |
Man page
|
| getSpatAnnCenter |
Man page
|
| getSpatAnnCenter,SPATA2-method |
Man page
|
| getSpatAnnCenter,SpatialAnnotation-method |
Man page
|
| getSpatAnnCenter,SpatialData-method |
Man page
|
| getSpatAnnCenterBcsp |
Man page
|
| getSpatAnnCenters |
Man page
|
| getSpatAnnCenters,SPATA2-method |
Man page
|
| getSpatAnnCenters,SpatialAnnotation-method |
Man page
|
| getSpatAnnCenters,SpatialData-method |
Man page
|
| getSpatAnnIds |
Man page
|
| getSpatAnnIds,ANY-method |
Man page
|
| getSpatAnnIds,SpatialData-method |
Man page
|
| getSpatAnnOutlineDf |
Man page
|
| getSpatAnnOutlineDf,SPATA2-method |
Man page
|
| getSpatAnnOutlineDf,SpatialAnnotation-method |
Man page
|
| getSpatAnnOutlineDf,SpatialData-method |
Man page
|
| getSpatAnnRange |
Man page
|
| getSpatAnnRange,SPATA2-method |
Man page
|
| getSpatAnnRange,SpatialData-method |
Man page
|
| getSpatAnnSf |
Man page
|
| getSpatAnnTags |
Man page
|
| getSpatAnnTags,SPATA2-method |
Man page
|
| getSpatAnnTags,SpatialData-method |
Man page
|
| getSpatSegmVarNames |
Man page
|
| getSpataDf |
Man page
|
| getSpataDir |
Man page
|
| getSpatialAnnotation |
Man page
|
| getSpatialAnnotation,SPATA2-method |
Man page
|
| getSpatialAnnotation,SpatialData-method |
Man page
|
| getSpatialAnnotations |
Man page
|
| getSpatialAnnotations,SPATA2-method |
Man page
|
| getSpatialAnnotations,SpatialData-method |
Man page
|
| getSpatialData |
Man page
|
| getSpatialMethod |
Man page
|
| getSpatialMethod,SPATA2-method |
Man page
|
| getSpatialMethod,SpatialData-method |
Man page
|
| getSpatialTrajectories |
Man page
|
| getSpatialTrajectory |
Man page
|
| getSpatialTrajectoryIds |
Man page
|
| getSpotSize |
Man page
|
| getSpotSize,SPATA2-method |
Man page
|
| getSpotSize,SpatialData-method |
Man page
|
| getStsDf |
Man page
|
| getTissueArea |
Man page
|
| getTissueOutlineCentroid |
Man page
|
| getTissueOutlineCentroid,HistoImage-method |
Man page
|
| getTissueOutlineCentroid,SpatialData-method |
Man page
|
| getTissueOutlineDf |
Man page
|
| getTissueOutlineDf,HistoImage-method |
Man page
|
| getTissueOutlineDf,SPATA2-method |
Man page
|
| getTissueOutlineDf,SpatialData-method |
Man page
|
| getTissueSections |
Man page
|
| getTrajectory |
Man page
Source code
|
| getTrajectoryDf |
Man page
Source code
|
| getTrajectoryIds |
Man page
Source code
|
| getTrajectoryLength |
Man page
|
| getTrajectoryNames |
Man page
Source code
|
| getTrajectoryObject |
Man page
Source code
|
| getTrajectoryScreeningDf |
Man page
Source code
|
| getTrajectorySegmentDf |
Man page
|
| getTrajectoryWidth |
Man page
|
| getTsneDf |
Man page
|
| getUmapDf |
Man page
|
| getVarTypeList |
Man page
|
| getVariableMolecules |
Man page
|
| getVariableNames |
Man page
|
| getWindowSize |
Man page
|
| getWindowSize,HistoImage-method |
Man page
|
| get_names_dummy |
Man page
Source code
|
| ggpInit |
Man page
Source code
|
| ggpLayerAxesClean |
Man page
Source code
|
| ggpLayerAxesSI |
Man page
Source code
|
| ggpLayerCaptureArea |
Man page
Source code
|
| ggpLayerColorGroupScale |
Man page
Source code
|
| ggpLayerEncirclingGroups |
Man page
Source code
|
| ggpLayerEncirclingSAS |
Man page
Source code
|
| ggpLayerExprEstimatesSAS |
Man page
Source code
|
| ggpLayerFixFrame |
Man page
Source code
|
| ggpLayerFrame |
Man page
Source code
|
| ggpLayerFrameByCoords |
Man page
Source code
|
| ggpLayerFrameByImage |
Man page
Source code
|
| ggpLayerGenePattern |
Source code
|
| ggpLayerGridVisiumHD |
Man page
Source code
|
| ggpLayerGroupOutline |
Man page
Source code
|
| ggpLayerHorizonSAS |
Man page
Source code
|
| ggpLayerImage |
Man page
|
| ggpLayerImage,HistoImage-method |
Man page
|
| ggpLayerImage,Image-method |
Man page
|
| ggpLayerImage,SPATA2-method |
Man page
|
| ggpLayerImage,SpatialAnnotation-method |
Man page
|
| ggpLayerImage,SpatialData-method |
Man page
|
| ggpLayerImage,data.frame-method |
Man page
|
| ggpLayerImageAnnotation |
Man page
Source code
|
| ggpLayerImgAnnBorder |
Man page
Source code
|
| ggpLayerPoints |
Man page
|
| ggpLayerPoints,SPATA2-method |
Man page
|
| ggpLayerPoints,SpatialData-method |
Man page
|
| ggpLayerPoints,data.frame-method |
Man page
|
| ggpLayerRect |
Man page
Source code
|
| ggpLayerSampleMask |
Man page
Source code
|
| ggpLayerSasEvaluation |
Source code
|
| ggpLayerScaleBarSI |
Man page
Source code
|
| ggpLayerScreeningDirectionSAS |
Man page
Source code
|
| ggpLayerSpatAnnOutline |
Man page
Source code
|
| ggpLayerSpatAnnPointer |
Man page
Source code
|
| ggpLayerSpatAnnRect |
Man page
Source code
|
| ggpLayerSpatialTrajectories |
Man page
|
| ggpLayerThemeCoords |
Man page
Source code
|
| ggpLayerTissueOutline |
Man page
|
| ggpLayerTissueOutline,HistoImage-method |
Man page
|
| ggpLayerTissueOutline,SPATA2-method |
Man page
|
| ggpLayerTissueOutline,SpatialData-method |
Man page
|
| ggpLayerTissueOutline,data.frame-method |
Man page
|
| ggpLayerTrajectories |
Man page
Source code
|
| ggpLayerTrajectoryFrame |
Man page
|
| ggpLayerZoom |
Man page
|
| ggpLayer_dummy |
Man page
Source code
|
| ggplot_dummy |
Man page
Source code
|
| ggplot_family |
Man page
Source code
|
| hide_unit |
Source code
|
| hlpr_adjust_legend_size |
Source code
|
| hlpr_assign_arguments |
Source code
|
| hlpr_breaks |
Source code
|
| hlpr_dist_mtr_to_df |
Source code
|
| hlpr_drop_all_na |
Source code
|
| hlpr_gene_set_name |
Source code
|
| hlpr_image_add_on |
Source code
|
| hlpr_image_add_on2 |
Source code
|
| hlpr_image_to_df |
Source code
|
| hlpr_join_with_color_by |
Source code
|
| hlpr_labs_add_on |
Source code
|
| hlpr_normalize_imap |
Source code
|
| hlpr_normalize_vctr |
Source code
|
| hlpr_one_distinct |
Source code
|
| hlpr_save_spata_object |
Source code
|
| hlpr_scatterplot |
Source code
|
| hlpr_smooth |
Source code
|
| hlpr_smooth_shiny |
Source code
|
| hlpr_subset_across |
Source code
|
| hlpr_transfer_slot_content |
Source code
|
| hlpr_vector_projection |
Man page
Source code
|
| hlpr_widen_trajectory_df |
Source code
|
| htmlAddHelper |
Source code
|
| htmlArrowButton |
Source code
|
| htmlBreak |
Source code
|
| htmlH5 |
Source code
|
| idSA |
Man page
Source code
|
| idST |
Man page
Source code
|
| identifyBackgroundColor |
Man page
|
| identifyBackgroundColor,HistoImage-method |
Man page
|
| identifyBackgroundColor,SPATA2-method |
Man page
|
| identifyBackgroundColor,SpatialData-method |
Man page
|
| identifyPixelContent |
Man page
|
| identifyPixelContent,HistoImage-method |
Man page
|
| identifyPixelContent,Image-method |
Man page
|
| identifyPixelContent,SPATA2-method |
Man page
|
| identifyPixelContent,SpatialData-method |
Man page
|
| identifySpatialOutliers |
Man page
Source code
|
| identifyTissueOutline |
Man page
|
| identifyTissueOutline,HistoImage-method |
Man page
|
| identifyTissueOutline,SPATA2-method |
Man page
|
| identifyTissueOutline,SpatialData-method |
Man page
|
| identifyTissueSections |
Man page
Source code
|
| identifyVariableMolecules |
Man page
Source code
|
| identify_artefact_threshold |
Source code
|
| identify_obs_in_polygon |
Man page
Source code
|
| identify_obs_in_spat_ann |
Man page
Source code
|
| identify_zero_inflated_variables |
Source code
|
| if_null |
Source code
|
| image_dummy |
Man page
Source code
|
| img_ann_highlight_group_button |
Source code
|
| include_tissue_outline |
Man page
Source code
|
| increase_n_data_points |
Man page
Source code
|
| increase_polygon_vertices |
Man page
Source code
|
| infer_gradient |
Source code
|
| initiateSpataObject |
Man page
Source code
|
| initiateSpataObjectEmpty |
Source code
|
| initiateSpataObjectMERFISH |
Man page
Source code
|
| initiateSpataObjectSlideSeqV1 |
Man page
|
| initiateSpataObjectVisium |
Man page
|
| initiateSpataObjectVisiumHD |
Man page
|
| initiateSpataObjectXenium |
Man page
|
| initiate_plot |
Source code
|
| interpolate_points_along_path |
Man page
Source code
|
| intersect_polygons |
Man page
Source code
|
| isDirVisium |
Man page
Source code
|
| isFeature |
Source code
|
| isGene |
Source code
|
| isGeneSet |
Source code
|
| isNumericVariable |
Source code
|
| isSPATA2 |
Man page
Source code
|
| isSpatialTrajectory |
Source code
|
| isTrajectory |
Source code
|
| is_area |
Man page
Source code
|
| is_area_pixel |
Man page
Source code
|
| is_area_si |
Man page
Source code
|
| is_dist |
Man page
Source code
|
| is_dist_pixel |
Man page
Source code
|
| is_dist_si |
Man page
Source code
|
| is_exclam |
Source code
|
| is_image_dir |
Source code
|
| is_inside_plg |
Man page
Source code
|
| is_number |
Source code
|
| is_numeric_input |
Source code
|
| is_outlier |
Man page
Source code
|
| is_percentage |
Source code
|
| is_spatial_measure |
Source code
|
| is_unit_area |
Man page
Source code
|
| is_unit_dist |
Man page
Source code
|
| joinWith |
Man page
Source code
|
| joinWithFeatures |
Man page
Source code
|
| joinWithGeneSets |
Man page
Source code
|
| joinWithGenes |
Man page
Source code
|
| joinWithPca |
Man page
Source code
|
| joinWithTsne |
Man page
Source code
|
| joinWithUmap |
Man page
Source code
|
| joinWithVariables |
Man page
Source code
|
| labsNone |
Man page
Source code
|
| lastImageAnnotation |
Man page
Source code
|
| lastSpatialAnnotation |
Source code
|
| legendBottom |
Man page
|
| legendColor |
Man page
Source code
|
| legendLeft |
Man page
|
| legendNone |
Man page
|
| legendRight |
Man page
|
| legendTop |
Man page
|
| loadExampleObject |
Man page
Source code
|
| loadImage |
Man page
|
| loadImage,HistoImage-method |
Man page
|
| loadImage,SPATA2-method |
Man page
|
| loadImage,SpatialData-method |
Man page
|
| loadImageDefault |
Man page
Source code
|
| loadImageHighres |
Man page
Source code
|
| loadImageLowres |
Man page
Source code
|
| loadImages |
Man page
|
| loadImages,SPATA2-method |
Man page
|
| loadImages,SpatialData-method |
Man page
|
| loadSpataObject |
Man page
Source code
|
| load_adata_matrix |
Source code
|
| load_adata_matrix_converter |
Source code
|
| lump_groups |
Source code
|
| mSwitch |
Source code
|
| makeContent.resizingSegmentsGrob |
Man page
Source code
|
| makeContent.resizingTextGrob |
Man page
Source code
|
| make_angle_bins |
Source code
|
| make_binary_image |
Man page
Source code
|
| make_bins |
Source code
|
| make_orthogonal_segment |
Man page
Source code
|
| make_orthogonal_segments |
Man page
Source code
|
| make_pixel_dataframe |
Source code
|
| make_scattermore_add_on |
Source code
|
| make_sf_polygon |
Source code
|
| make_traj_rect |
Source code
|
| make_unique_molecules |
Source code
|
| mapSpatialAnnotationTags |
Man page
Source code
|
| map_to_tissue_section |
Man page
Source code
|
| matrix_dummy |
Man page
Source code
|
| mergeGroups |
Man page
Source code
|
| mergeSpatialAnnotations |
Man page
Source code
|
| mergeTissueSections |
Man page
Source code
|
| mergeWithTissueOutline |
Man page
Source code
|
| merge_cnv_bins |
Source code
|
| merge_intersecting_polygons |
Man page
Source code
|
| method_hclust |
Man page
Source code
|
| model_ascending |
Man page
Source code
|
| model_descending |
Man page
Source code
|
| model_peak |
Man page
Source code
|
| model_trough |
Man page
Source code
|
| moduleAddGeneSetsServer |
Man page
Source code
|
| moduleAddGeneSetsUI |
Man page
Source code
|
| moduleSurfacePlotServer |
Man page
Source code
|
| moduleSurfacePlotUI |
Man page
Source code
|
| nBarcodes |
Source code
|
| nCounts |
Source code
|
| nGenes |
Man page
Source code
|
| nImageDims |
Source code
|
| nImages |
Man page
Source code
|
| nMetabolites |
Man page
Source code
|
| nMolecules |
Man page
Source code
|
| nObs |
Man page
Source code
|
| nProteins |
Man page
Source code
|
| nSpatialAnnotations |
Man page
|
| nSpatialAnnotations,SPATA2-method |
Man page
|
| nSpatialAnnotations,SpatialData-method |
Man page
|
| nSpatialTrajectories |
Man page
Source code
|
| nTrajectories |
Man page
Source code
|
| next_divisible |
Source code
|
| normalize |
Man page
|
| normalizeCounts |
Man page
Source code
|
| normalize_smrd_projection_df |
Source code
|
| normalize_variables |
Source code
|
| numericSlider |
Source code
|
| objectMemoryUsage |
Source code
|
| object_dummy |
Man page
Source code
|
| obsUnit |
Man page
|
| obsUnit,ANY-method |
Man page
|
| obsUnit,SpatialMethod-method |
Man page
|
| order_df |
Source code
|
| padd_image |
Source code
|
| pb_dummy |
Man page
Source code
|
| pick_vars |
Source code
|
| pixel_df_to_image |
Source code
|
| plotAutoencoderAssessment |
Man page
Source code
|
| plotAutoencoderResults |
Man page
Source code
|
| plotBarchart |
Man page
Source code
|
| plotBoxplot |
Man page
Source code
|
| plotCnvDotplot |
Source code
|
| plotCnvHeatmap |
Man page
Source code
|
| plotCnvLineplot |
Man page
Source code
|
| plotCnvResults |
Man page
Source code
|
| plotDeaDotPlot |
Man page
Source code
|
| plotDeaHeatmap |
Man page
Source code
|
| plotDeaVolcano |
Man page
Source code
|
| plotDeaVolcano1v1 |
Man page
Source code
|
| plotDendrogram |
Man page
Source code
|
| plotDensityplot |
Man page
|
| plotExprVsDistSA |
Man page
|
| plotExprVsDistST |
Man page
|
| plotGeneDendrogram |
Man page
Source code
|
| plotGseaDotPlot |
Man page
Source code
|
| plotHistogram |
Man page
Source code
|
| plotImage |
Man page
|
| plotImage,HistoImage-method |
Man page
|
| plotImage,Image-method |
Man page
|
| plotImage,SPATA2-method |
Man page
|
| plotImage,SpatialData-method |
Man page
|
| plotImageAnnotations |
Man page
Source code
|
| plotImageBase |
Man page
|
| plotImageBase,HistoImage-method |
Man page
|
| plotImageBase,Image-method |
Man page
|
| plotImageBase,SPATA2-method |
Man page
|
| plotImageBase,SpatialData-method |
Man page
|
| plotImageMask |
Man page
|
| plotImageMask,HistoImage-method |
Man page
|
| plotImageMask,SPATA2-method |
Man page
|
| plotImageMask,SpatialData-method |
Man page
|
| plotImages |
Man page
|
| plotImages,SPATA2-method |
Man page
|
| plotImages,SpatialData-method |
Man page
|
| plotLoglik |
Man page
Source code
|
| plotMolecules2D |
Man page
Source code
|
| plotMosaicplot |
Man page
Source code
|
| plotOverview |
Man page
|
| plotOverview,SpatialAnnotationScreening-method |
Man page
|
| plotOverview,SpatialTrajectoryScreening-method |
Man page
|
| plotPCA |
Man page
Source code
|
| plotPca |
Man page
Source code
|
| plotPcaElbow |
Man page
|
| plotPcaVariation |
Man page
Source code
|
| plotPixelContent |
Man page
|
| plotPixelContent,HistoImage-method |
Man page
|
| plotPixelContent,SPATA2-method |
Man page
|
| plotPixelContent,SpatialData-method |
Man page
|
| plotRidgeplot |
Man page
Source code
|
| plotRiverplot |
Man page
Source code
|
| plotSasBarplot |
Man page
Source code
|
| plotSasDensityplot |
Man page
Source code
|
| plotSasHeatmap |
Man page
Source code
|
| plotSasLineplot |
Man page
Source code
|
| plotSasRidgeplot |
Man page
Source code
|
| plotScatterplot |
Man page
Source code
|
| plotSpatialAnnotations |
Man page
|
| plotSpatialAnnotations,SPATA2-method |
Man page
|
| plotSpatialAnnotations,SpatialData-method |
Man page
|
| plotSpatialTrajectories |
Man page
|
| plotStatisticsInteractive |
Man page
|
| plotStsBarplot |
Man page
|
| plotStsHeatmap |
Man page
|
| plotStsLineplot |
Man page
|
| plotStsRidgeplot |
Man page
|
| plotSurface |
Man page
|
| plotSurface,SPATA2-method |
Man page
|
| plotSurface,SpatialAnnotationScreening-method |
Man page
|
| plotSurface,SpatialGradientScreening-method |
Man page
|
| plotSurface,data.frame-method |
Man page
|
| plotSurfaceBase |
Man page
Source code
|
| plotSurfaceComparison |
Man page
|
| plotSurfaceComparison,SPATA2-method |
Man page
|
| plotSurfaceComparison,data.frame-method |
Man page
|
| plotSurfaceInteractive |
Man page
Source code
|
| plotSurfaceInteractiveDiet |
Source code
|
| plotSurfaceQuantiles |
Man page
Source code
|
| plotSurfaceSAS |
Man page
|
| plotSurfaceSAS,SPATA2-method |
Man page
|
| plotSurfaceSAS,SpatialAnnotationScreening-method |
Man page
|
| plotSurfaceSC |
Man page
Source code
|
| plotTSNE |
Man page
Source code
|
| plotTrajectoryBarplot |
Man page
Source code
|
| plotTrajectoryHeatmap |
Man page
Source code
|
| plotTrajectoryLineplot |
Man page
Source code
|
| plotTrajectoryRidgeplot |
Man page
Source code
|
| plotTsne |
Man page
Source code
|
| plotTsneComparison |
Man page
Source code
|
| plotUMAP |
Man page
Source code
|
| plotUmap |
Man page
Source code
|
| plotUmapComparison |
Man page
Source code
|
| plotVioBoxplot |
Man page
Source code
|
| plotViolinplot |
Man page
Source code
|
| plotVolcano |
Man page
|
| plotVolcano,SpatialAnnotationScreening-method |
Man page
|
| plotVolcano,SpatialTrajectoryScreening-method |
Man page
|
| plot_mae |
Source code
|
| plot_model_comparison_dotplot |
Man page
Source code
|
| plot_overview |
Source code
|
| plot_polygon |
Source code
|
| plot_polygon_overlap |
Source code
|
| plot_screening_evaluation |
Man page
Source code
|
| plot_sgs_barplot |
Source code
|
| plot_sgs_densityplot |
Source code
|
| plot_sgs_heatmap |
Source code
|
| plot_sgs_lineplot |
Source code
|
| plot_sgs_ridgeplot |
Source code
|
| plot_type_dummy |
Man page
Source code
|
| polygon_inside_polygon |
Man page
Source code
|
| polygon_intersects_polygon |
Man page
Source code
|
| prepare_coords_df_visium_hd |
Man page
Source code
|
| printAutoencoderSummary |
Man page
Source code
|
| printDefaultInstructions |
Man page
Source code
|
| printGeneSetOverview |
Man page
Source code
|
| print_family |
Man page
Source code
|
| processImage |
Man page
Source code
|
| process_angle_justification |
Source code
|
| process_axis |
Source code
|
| process_coords_df_sa |
Source code
|
| process_coords_df_sa2 |
Source code
|
| process_expand_input |
Man page
Source code
|
| process_outline_df |
Source code
|
| process_pixel_scale_factor |
Source code
|
| process_ranges |
Man page
Source code
|
| process_sce_bayes_space |
Source code
|
| process_transform_with |
Source code
|
| project_on_trajectory |
Man page
Source code
|
| project_on_vector |
Man page
Source code
|
| pull_slot |
Source code
|
| random_positions_with_periods |
Source code
|
| random_positions_within_period |
Source code
|
| read_coords |
Man page
Source code
|
| read_coords_merfish |
Man page
Source code
|
| read_coords_slide_seq_v1 |
Man page
|
| read_coords_visium |
Man page
|
| read_coords_xenium |
Man page
|
| read_matrix_from_folder |
Man page
|
| recAlpha |
Man page
|
| recDbscanEps |
Man page
|
| recDbscanMinPts |
Man page
|
| recSgsRes |
Man page
|
| reduceResolutionVisiumHD |
Man page
|
| reduceSpataObject |
Man page
|
| reduce_coords_df_visium_hd |
Man page
|
| reduce_vec |
Man page
|
| refImage |
Man page
|
| refImage,SPATA2-method |
Man page
|
| refImage,SpatialData-method |
Man page
|
| regexes |
Man page
|
| registerImage |
Man page
|
| registerImage,SPATA2-method |
Man page
|
| registerImage,SpatialData-method |
Man page
|
| relateToSpatialAnnotation |
Man page
Source code
|
| relevelGroups |
Man page
|
| removeGenes |
Man page
|
| removeGenesMitochondrial |
Man page
|
| removeGenesRibosomal |
Man page
|
| removeGenesStress |
Man page
|
| removeGenesZeroCounts |
Man page
|
| removeImage |
Man page
|
| removeImage,SPATA2-method |
Man page
|
| removeImage,SpatialData-method |
Man page
|
| removeMetaFeatures |
Man page
|
| removeMolecules |
Man page
|
| removeObs |
Man page
|
| removeObsZeroCounts |
Man page
|
| removeProcessedMatrix |
Man page
|
| removeSignatures |
Man page
|
| removeSpatialAnnotations |
Man page
|
| removeSpatialOutliers |
Man page
|
| removeSpatialTrajectories |
Man page
|
| removeTissueFragments |
Man page
|
| remove_stress_and_mt_genes |
Source code
|
| renameGroups |
Man page
|
| renameImage |
Man page
|
| renameImage,SPATA2-method |
Man page
|
| renameImage,SpatialData-method |
Man page
|
| renameMetaFeatures |
Man page
|
| renameMolecularAssay |
Man page
|
| renameSpataObject |
Man page
|
| renameSpatialAnnotation |
Man page
|
| renameSpatialTrajectory |
Man page
|
| renameTissueSection |
Man page
|
| resetImageJustification |
Man page
Source code
|
| resetImageTransformations |
Man page
|
| resetImageTransformations,HistoImage-method |
Man page
|
| resetImageTransformations,SPATA2-method |
Man page
|
| resetImageTransformations,SpatialData-method |
Man page
|
| resizeImage |
Man page
|
| resizeImage,HistoImage-method |
Man page
|
| resizeImage,SPATA2-method |
Man page
|
| resizeImage,SpatialData-method |
Man page
|
| resizingSegmentsGrob |
Man page
|
| resizingTextGrob |
Man page
|
| rotateAll |
Man page
|
| rotateCoordinates |
Man page
|
| rotateCoordsDf |
Man page
|
| rotateImage |
Man page
|
| rotateSpatialAnnotation |
Man page
|
| rotateSpatialAnnotation,SPATA2-method |
Man page
|
| rotateSpatialAnnotation,SpatialData-method |
Man page
|
| rotateSpatialAnnotations |
Man page
|
| rotateSpatialTrajectories |
Man page
|
| rotateTissueOutlineDf |
Man page
|
| rotate_coords_df |
Man page
|
| runAutoencoderAssessment |
Man page
Source code
|
| runAutoencoderDenoising |
Man page
Source code
|
| runBayesSpaceClustering |
Man page
Source code
|
| runCIN |
Man page
|
| runCNV |
Man page
|
| runCnvAnalysis |
Man page
|
| runDEA |
Man page
|
| runDeAnalysis |
Man page
|
| runGSEA |
Man page
|
| runKmeansClustering |
Man page
|
| runNearestNeighborClustering |
Man page
|
| runPCA |
Man page
|
| runPca |
Man page
|
| runSDEA |
Man page
|
| runSPARKX |
Man page
|
| runSPROD |
Man page
Source code
|
| runSeuratClustering |
Man page
|
| runSpatialCorrelationAnalysis |
Man page
Source code
|
| runTSNE |
Man page
|
| runTsne |
Man page
|
| runUMAP |
Man page
|
| runUmap |
Man page
|
| sample_name |
Man page
Source code
|
| saveSpataObject |
Man page
Source code
|
| scale_color_add_on |
Man page
|
| scale_coords_df |
Man page
Source code
|
| scale_image |
Source code
|
| scale_nuclei_df |
Source code
|
| section_dummy |
Man page
Source code
|
| segments_to_vertices |
Man page
Source code
|
| setActiveExpressionMatrix |
Man page
Source code
|
| setActiveMatrix |
Man page
Source code
|
| setAssay |
Man page
Source code
|
| setAutoencoderAssessment |
Man page
Source code
|
| setBarcodes |
Man page
Source code
|
| setCCD |
Man page
Source code
|
| setCaptureArea |
Man page
|
| setCaptureArea,SPATA2-method |
Man page
|
| setCaptureArea,SpatialData-method |
Man page
|
| setCnvResults |
Man page
Source code
|
| setCoordsDf |
Man page
|
| setCoordsDf,SPATA2-method |
Man page
|
| setCoordsDf,SpatialData-method |
Man page
|
| setCountMatrix |
Man page
Source code
|
| setDeaResultsDf |
Source code
|
| setDefault |
Man page
Source code
|
| setDefaultInstructions |
Man page
Source code
|
| setDenoisedMatrix |
Man page
Source code
|
| setDirectoryInstructions |
Man page
Source code
|
| setFeatureDf |
Source code
|
| setHistoImage |
Man page
|
| setHistoImage,SPATA2-method |
Man page
|
| setHistoImage,SpatialData-method |
Man page
|
| setImage |
Man page
Source code
|
| setImageAnnotation |
Man page
Source code
|
| setImageAnnotations |
Man page
Source code
|
| setImageDir |
Man page
|
| setImageDir,HistoImage-method |
Man page
|
| setImageDir,SPATA2-method |
Man page
|
| setImageDir,SpatialData-method |
Man page
|
| setImageTransformations |
Man page
|
| setImageTransformations,SpatialData-method |
Man page
|
| setLogfileDf |
Man page
Source code
|
| setMetaDf |
Man page
Source code
|
| setMetaVarDf |
Man page
Source code
|
| setPcaDf |
Man page
Source code
|
| setPrResults |
Man page
Source code
|
| setProcessedMatrix |
Man page
Source code
|
| setScaleFactor |
Man page
|
| setScaleFactor,HistoImage-method |
Man page
|
| setScaleFactor,SPATA2-method |
Man page
|
| setScaleFactor,SpatialData-method |
Man page
|
| setSpCorResults |
Man page
Source code
|
| setSpataDir |
Man page
Source code
|
| setSpatialAnnotation |
Man page
|
| setSpatialAnnotation,SPATA2-method |
Man page
|
| setSpatialAnnotations |
Man page
|
| setSpatialAnnotations,SPATA2-method |
Man page
|
| setSpatialData |
Man page
Source code
|
| setSpatialMethod |
Man page
|
| setSpatialMethod,SPATA2-method |
Man page
|
| setSpatialMethodInfo |
Man page
Source code
|
| setSpatialMethodSlot |
Man page
Source code
|
| setSpatialTrajectories |
Man page
Source code
|
| setSpatialTrajectory |
Man page
Source code
|
| setTrajectories |
Man page
Source code
|
| setTrajectory |
Man page
Source code
|
| setTsneDf |
Man page
Source code
|
| setUmapDf |
Man page
Source code
|
| setUpMetaVar |
Man page
|
| setUpMetaVar,MolecularAssay-method |
Man page
|
| setUpMetaVar,SPATA2-method |
Man page
|
| set_dummy |
Man page
Source code
|
| seurat_object_dummy |
Man page
Source code
|
| shiftSpatialAnnotation |
Man page
Source code
|
| shift_for_evaluation |
Source code
|
| shift_for_plotting |
Source code
|
| shift_frame |
Source code
|
| shift_screening_df_to_long |
Source code
|
| shift_smrd_projection_df |
Source code
|
| shinyModuleZoomingServer |
Man page
Source code
|
| shinyModuleZoomingUI |
Man page
Source code
|
| showColorPalettes |
Man page
Source code
|
| showColorSpectra |
Man page
Source code
|
| showColors |
Man page
Source code
|
| showModels |
Man page
Source code
|
| si_dist_to_si_dist_fct |
Source code
|
| signatures |
Man page
|
| simulate_complete_coords_sa |
Source code
|
| simulate_expression_pattern_sas |
Man page
|
| simulate_expression_pattern_sts |
Man page
|
| simulate_random_expression |
Man page
|
| simulate_random_gradients |
Man page
|
| simulate_spatial_niches |
Man page
|
| smoothSpatialAnnotation |
Man page
|
| smoothSpatially |
Man page
|
| sort_into_components |
Man page
|
| spata2 |
Man page
|
| spata2-class |
Man page
|
| spatialAnnotationScreening |
Man page
|
| spatialAnnotationToGrouping |
Man page
|
| spatialTrajectoryScreening |
Man page
|
| spatial_gradient_screening |
Man page
|
| spatial_methods |
Man page
|
| spatial_trajectory |
Man page
|
| spatial_trajectory-class |
Man page
|
| splitSpataObject |
Man page
|
| subsetByBarcodes |
Man page
Source code
|
| subsetSpataObject |
Man page
|
| summarize_batch_reduce_visium_hd |
Man page
|
| summarize_formulas |
Man page
|
| tab_create_segmentation_return |
Source code
|
| tab_create_trajectories_return |
Source code
|
| tab_surface_plots_app |
Man page
Source code
|
| tab_surface_plots_return |
Man page
Source code
|
| tagSpatialAnnotations |
Man page
|
| tagSpatialAnnotations,SPATA2-method |
Man page
|
| tagSpatialAnnotations,SpatialData-method |
Man page
|
| test_fn |
Source code
|
| test_sas_input |
Source code
|
| test_save_in_logfile |
Source code
|
| textInputWrapper |
Source code
|
| theme_image |
Source code
|
| theme_lineplot_gradient |
Man page
Source code
|
| theme_ridgeplot_gradient |
Man page
Source code
|
| theme_trajectory_fit |
Man page
Source code
|
| theme_transparent |
Man page
Source code
|
| theme_void_custom |
Source code
|
| transfer_slot_content |
Man page
Source code
|
| transform_area_si_to_pixel |
Man page
Source code
|
| transform_area_si_to_pixels |
Man page
Source code
|
| transform_coords |
Man page
Source code
|
| transform_dist_si_to_pixel |
Man page
Source code
|
| transform_dist_si_to_pixels |
Man page
Source code
|
| transform_image |
Man page
Source code
|
| transform_outline |
Source code
|
| transform_pixel_to_area_si |
Man page
Source code
|
| transform_pixel_to_dist_si |
Man page
Source code
|
| transform_pixel_to_si |
Man page
Source code
|
| transform_pixels_to_area_si |
Man page
Source code
|
| transform_pixels_to_dist_si |
Man page
Source code
|
| translate_shape_string |
Man page
Source code
|
| true_if_null |
Source code
|
| tutorial_hint_dummy |
Man page
Source code
|
| unloadImage |
Man page
|
| unloadImage,HistoImage-method |
Man page
|
| unloadImage,SPATA2-method |
Man page
|
| unloadImage,SpatialData-method |
Man page
|
| unloadImages |
Man page
|
| unloadImages,SPATA2-method |
Man page
|
| unloadImages,SpatialData-method |
Man page
|
| unwindAggregation |
Man page
Source code
|
| updateS4 |
Man page
|
| updateS4,SpatialMethod-method |
Man page
|
| updateS4,spata2-method |
Man page
|
| updateSpataObject |
Man page
Source code
|
| update_dummy |
Man page
Source code
|
| update_s4_architecture_of_spata2_object |
Source code
|
| update_spata2v2_to_spata2v3 |
Man page
Source code
|
| useVarForTissueOutline |
Man page
Source code
|
| validActivationFunctions |
Man page
Source code
|
| validAgglomerationMethods |
Man page
Source code
|
| validAlluvialTypes |
Man page
Source code
|
| validColorPalettes |
Man page
Source code
|
| validColorSpectra |
Man page
Source code
|
| validDeaMethods |
Man page
Source code
|
| validDefaultInstructionSlots |
Man page
Source code
|
| validDistanceMethods |
Man page
Source code
|
| validHierarchicalClusterMethods |
Man page
Source code
|
| validModelNames |
Man page
Source code
|
| validPadjMethods |
Man page
Source code
|
| validSpatialMethods |
Man page
Source code
|
| validUnits |
Man page
Source code
|
| validUnitsOfArea |
Man page
Source code
|
| validUnitsOfAreaSI |
Man page
Source code
|
| validUnitsOfLength |
Man page
Source code
|
| validUnitsOfLengthSI |
Man page
Source code
|
| validate_only_one_arg_specified |
Source code
|
| validation |
Man page
Source code
|
| variable |
Man page
Source code
|
| variable_num |
Man page
Source code
|
| variables_num |
Man page
Source code
|
| version_string |
Source code
|
| visiumSpotDistances |
Man page
Source code
|
| visium_spots |
Man page
|
| vselect |
Man page
|
| waive_if_null |
Source code
|
| whichSpaceRangerVersion |
Source code
|
| whichTissueSection |
Man page
Source code
|
| writeImage |
Man page
|
| writeImage,HistoImage-method |
Man page
|
| writeImage,SPATA2-method |
Man page
|
| writeImage,SpatialData-method |
Man page
|
