| GeomPointFixed |
Man page
|
| GeomSegmentFixed |
Man page
|
| GeomTextFixed |
Man page
|
| HistologyImage |
Man page
|
| HistologyImage-class |
Man page
|
| HistologyImaging |
Man page
|
| HistologyImaging-class |
Man page
|
| ImageAnnotation |
Man page
|
| ImageAnnotation-class |
Man page
|
| ImageAnnotationScreening |
Man page
|
| ImageAnnotationScreening-class |
Man page
|
| SpatialMethod |
Man page
|
| SpatialMethod-class |
Man page
|
| SpatialSegment |
Man page
|
| SpatialSegment-class |
Man page
|
| SpatialSegmentation |
Man page
|
| SpatialSegmentation-class |
Man page
|
| SpatialTrajectory |
Man page
|
| SpatialTrajectory-class |
Man page
|
| SpatialTrajectoryScreening |
Man page
|
| SpatialTrajectoryScreening-class |
Man page
|
| Trajectory |
Man page
|
| Trajectory-class |
Man page
|
| Visium |
Man page
|
| Visium-class |
Man page
|
| across |
Man page
Source code
|
| across_dummy |
Man page
Source code
|
| addAutoencoderSetUp |
Man page
Source code
|
| addExpressionMatrix |
Man page
Source code
|
| addFeatures |
Man page
Source code
|
| addGeneFeatures |
Man page
Source code
|
| addGeneMetaData |
Man page
Source code
|
| addGeneSet |
Man page
Source code
|
| addGeneSetsInteractive |
Man page
Source code
|
| addImageAnnotation |
Man page
Source code
|
| addImageDir |
Man page
Source code
|
| addPointsBase |
Man page
Source code
|
| addSegmentationVariable |
Man page
Source code
|
| addSpCorCluster |
Man page
Source code
|
| addSpatialTrajectory |
Man page
Source code
|
| addTrajectoryObject |
Source code
|
| add_dbscan_variable |
Man page
Source code
|
| add_helper |
Source code
|
| add_models |
Man page
Source code
|
| add_models_to_shifted_projection_df |
Source code
|
| add_outline_variable |
Man page
Source code
|
| add_tissue_section_variable |
Man page
Source code
|
| adjustDefaultInstructions |
Source code
|
| adjustDirectoryInstructions |
Man page
Source code
|
| adjustGeneSetDf |
Man page
Source code
|
| adjustGseaDf |
Source code
|
| alignImageAnnotation |
Man page
Source code
|
| alignSpatialTrajectory |
Man page
Source code
|
| allColorpalettes |
Man page
|
| allColorspectra |
Man page
|
| all_bcsp_distances |
Man page
Source code
|
| all_color_palettes |
Man page
|
| all_color_spectra |
Man page
|
| append_polygon_df |
Man page
Source code
|
| are_all_area_or_dist |
Man page
Source code
|
| argument_dummy |
Man page
Source code
|
| arrange_as_polygon |
Man page
Source code
|
| arrange_by_outline_variable |
Source code
|
| asGiotto |
Man page
Source code
|
| asHistologyImage |
Man page
|
| asHistologyImage,VisiumV1-method |
Man page
|
| asHistologyImaging |
Man page
|
| asHistologyImaging,AnnDataR6-method |
Man page
|
| asHistologyImaging,VisiumV1-method |
Man page
|
| asPixel |
Source code
|
| asSPATA2 |
Man page
|
| asSPATA2,AnnDataR6-method |
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
|
| asUnit |
Source code
|
| asVisiumV1 |
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
|
| assessTrajectoryTrends |
Source code
|
| assessTrajectoryTrends2 |
Source code
|
| assessTrajectoryTrendsCustomized |
Source code
|
| assessTrajectoryTrendsCustomized2 |
Source code
|
| attachUnit |
Man page
Source code
|
| attach_uni |
Man page
|
| average_genes |
Man page
Source code
|
| barcodesToImageAnnotation |
Man page
Source code
|
| bin_by_angle |
Man page
Source code
|
| bin_by_area |
Source code
|
| bin_by_expansion |
Man page
Source code
|
| bin_projection_df |
Source code
|
| binwidth_dummy |
Man page
Source code
|
| br_add |
Source code
|
| breaks |
Source code
|
| buffer_area |
Man page
Source code
|
| cds_dummy |
Man page
Source code
|
| checkShortcut |
Source code
|
| check_all_barcodes |
Man page
Source code
|
| check_assign |
Man page
Source code
|
| check_atdf |
Man page
Source code
|
| check_availability |
Man page
Source code
|
| check_binwidth_n_bins |
Source code
|
| check_color_to |
Man page
Source code
|
| check_compiled_trajectory_df |
Man page
Source code
|
| check_coordinate_variables |
Man page
Source code
|
| check_coords_df |
Man page
Source code
|
| check_customized_trends |
Man page
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_ias_input |
Source code
|
| check_image_annotation_ids |
Source code
|
| check_image_annotation_tags |
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 |
Man page
Source code
|
| check_pattern |
Man page
Source code
|
| check_pt |
Man page
Source code
|
| check_rtdf |
Man page
Source code
|
| check_sample |
Man page
Source code
|
| check_saving |
Man page
Source code
|
| check_segment |
Man page
Source code
|
| check_slot_coordinates |
Man page
Source code
|
| check_slot_data |
Man page
Source code
|
| check_slot_dim_red |
Man page
Source code
|
| check_slot_fdata |
Man page
Source code
|
| check_slot_image |
Man page
Source code
|
| check_slot_samples |
Man page
Source code
|
| check_slot_scvelo |
Man page
Source code
|
| check_slot_trajectories |
Man page
Source code
|
| check_slot_used_genesets |
Man page
Source code
|
| check_slot_version |
Man page
Source code
|
| check_smooth |
Man page
Source code
|
| check_spata_df |
Man page
Source code
|
| check_spatial_data |
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_trajectory_object |
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
|
| clustering |
Man page
|
| cnv_ref |
Man page
|
| cnv_regions_df |
Man page
|
| color_vector |
Man page
|
| computeCnvByChrArm |
Man page
Source code
|
| computeGeneMetaData |
Man page
Source code
|
| computeGeneMetaData2 |
Man page
Source code
|
| computeGeneNormality |
Source code
|
| compute_angle_between_two_points |
Man page
Source code
|
| compute_distance |
Man page
Source code
|
| concatenate_polypaths |
Source code
|
| container |
Source code
|
| containsCNV |
Man page
Source code
|
| containsHistologyImage |
Man page
Source code
|
| containsHistologyImaging |
Man page
Source code
|
| containsImage |
Man page
Source code
|
| containsImageObject |
Man page
Source code
|
| containsPixelScaleFactor |
Man page
Source code
|
| containsTissueOutline |
Source code
|
| countImageAnnotationTags |
Man page
Source code
|
| createHistologyImage |
Source code
|
| createHistologyImaging |
Man page
|
| createImageAnnotations |
Man page
|
| createImageObject |
Source code
|
| createSegmentation |
Man page
Source code
|
| createSpatialSegmentation |
Man page
|
| createSpatialTrajectories |
Man page
|
| create_encircling_add_on |
Source code
|
| create_image_annotations_ui |
Source code
|
| create_model_df |
Man page
Source code
|
| cropSpataObject |
Man page
Source code
|
| currentSpata2Version |
Man page
Source code
|
| data_counts |
Man page
|
| data_counts-class |
Man page
|
| dea |
Man page
|
| 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 |
Man page
Source code
|
| discardFeatures |
Man page
Source code
|
| discardGeneFeatures |
Man page
Source code
|
| discardGeneSets |
Man page
Source code
|
| discardGenes |
Man page
Source code
|
| discardImageAnnotations |
Man page
Source code
|
| discardSegmentationVariable |
Man page
Source code
|
| discardSpatialTrajectory |
Source code
|
| downloadPubExample |
Man page
Source code
|
| downloadRawData |
Man page
|
| downloadSpataObject |
Man page
|
| downloadSpataObjects |
Man page
|
| dropped_df_dummy |
Man page
Source code
|
| enhanceSpataObject |
Source code
|
| evaluate_model_fits |
Source code
|
| examineClusterResults |
Man page
Source code
|
| examineTrajectoryAssessment |
Source code
|
| exchangeImage |
Man page
Source code
|
| expand_image_range |
Source code
|
| expand_image_side |
Source code
|
| export |
Man page
Source code
|
| extract_unit |
Man page
Source code
|
| extract_value |
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_percentage_input |
Source code
|
| feedback_pos |
Source code
|
| feedback_range_input |
Source code
|
| feedback_spatial_measure |
Source code
|
| filterDeaDf |
Man page
Source code
|
| filterTrajectoryTrends |
Source code
|
| filterTrends |
Source code
|
| filter_by_best |
Source code
|
| filter_by_model |
Source code
|
| filter_by_thresholds |
Source code
|
| findMonocleClusters |
Man page
Source code
|
| findNearestNeighbourClusters |
Man page
Source code
|
| findSeuratClusters |
Man page
Source code
|
| find_elbow_point |
Source code
|
| flexible_call_dummy |
Man page
Source code
|
| flipAll |
Man page
Source code
|
| flipCoordinates |
Man page
Source code
|
| flipCoords |
Man page
Source code
|
| flipCoordsDf |
Man page
Source code
|
| flipImage |
Man page
Source code
|
| flipImageAnnotations |
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
|
| getActiveExpressionMatrixName |
Man page
Source code
|
| getActiveMatrixName |
Man page
Source code
|
| getAutoencoderAssessment |
Man page
Source code
|
| getAutoencoderSetUp |
Man page
Source code
|
| getBarcodeSpotDistance |
Man page
Source code
|
| getBarcodeSpotDistances |
Man page
Source code
|
| getBarcodes |
Man page
Source code
|
| getBarcodesInPolygon |
Man page
Source code
|
| getBarcodesInPolygonList |
Man page
Source code
|
| getCCD |
Man page
Source code
|
| getChrRegionsDf |
Man page
Source code
|
| getCnvFeatureNames |
Man page
Source code
|
| getCnvGenesDf |
Man page
Source code
|
| getCnvResults |
Man page
Source code
|
| getCoordsCenter |
Man page
Source code
|
| getCoordsDf |
Man page
Source code
|
| getCoordsRange |
Man page
Source code
|
| getCountMatrix |
Man page
Source code
|
| getDeaGenes |
Man page
Source code
|
| getDeaLfcName |
Man page
Source code
|
| getDeaOverview |
Man page
Source code
|
| getDeaResultsDf |
Man page
Source code
|
| getDefault |
Man page
Source code
|
| getDefaultGrouping |
Man page
Source code
|
| getDefaultInstructions |
Man page
Source code
|
| getDefaultTrajectory |
Man page
Source code
|
| getDefaultTrajectoryId |
Man page
|
| getDimRedDf |
Man page
Source code
|
| getDirectoryInstructions |
Man page
Source code
|
| getExpressionMatrix |
Man page
Source code
|
| getExpressionMatrixNames |
Man page
Source code
|
| getFeatureDf |
Man page
Source code
|
| getFeatureNames |
Man page
Source code
|
| getFeatureValues |
Man page
Source code
|
| getFeatureVariables |
Man page
Source code
|
| getFromSeurat |
Man page
Source code
|
| getGeneCounts |
Man page
Source code
|
| getGeneDistDf |
Source code
|
| getGeneDistMtr |
Man page
Source code
|
| getGeneFeatureNames |
Man page
Source code
|
| getGeneMetaData |
Man page
Source code
|
| getGeneMetaDf |
Man page
Source code
|
| getGenePosDf |
Man page
Source code
|
| getGeneSetDf |
Man page
Source code
|
| getGeneSetList |
Man page
Source code
|
| getGeneSetOverview |
Man page
Source code
|
| getGeneSets |
Man page
Source code
|
| getGeneSetsInteractive |
Man page
Source code
|
| getGenes |
Man page
Source code
|
| getGenesInteractive |
Man page
Source code
|
| getGroupNames |
Man page
Source code
|
| getGroupingOptions |
Man page
Source code
|
| getGseaDf |
Man page
Source code
|
| getGseaResults |
Man page
Source code
|
| getIasBinAreas |
Man page
Source code
|
| getIasDf |
Man page
Source code
|
| getIasExpansion |
Man page
Source code
|
| getImage |
Man page
Source code
|
| getImageAnnotation |
Man page
Source code
|
| getImageAnnotationAreaDf |
Man page
Source code
|
| getImageAnnotationCenter |
Man page
Source code
|
| getImageAnnotationIds |
Man page
Source code
|
| getImageAnnotationScreeningDf |
Man page
Source code
|
| getImageAnnotationTags |
Source code
|
| getImageAnnotations |
Man page
Source code
|
| getImageCenter |
Man page
Source code
|
| getImageDf |
Man page
Source code
|
| getImageDims |
Man page
Source code
|
| getImageDir |
Man page
Source code
|
| getImageDirDefault |
Man page
Source code
|
| getImageDirHighres |
Man page
Source code
|
| getImageDirLowres |
Man page
Source code
|
| getImageDirectories |
Man page
Source code
|
| getImageInfo |
Man page
Source code
|
| getImageObject |
Man page
Source code
|
| getImageOrigin |
Man page
Source code
|
| getImageRange |
Man page
Source code
|
| getImageRaster |
Man page
Source code
|
| getImageRasterInfo |
Man page
Source code
|
| getImageSectionsByBarcode |
Man page
Source code
|
| getImgAnnArea |
Man page
Source code
|
| getImgAnnBarcodes |
Man page
Source code
|
| getImgAnnBorderDf |
Man page
Source code
|
| getImgAnnCenter |
Man page
|
| getImgAnnCenter,ImageAnnotation-method |
Man page
|
| getImgAnnCenter,spata2-method |
Man page
|
| getImgAnnCenterBcsp |
Man page
Source code
|
| getImgAnnCenters |
Man page
|
| getImgAnnCenters,ImageAnnotation-method |
Man page
|
| getImgAnnCenters,spata2-method |
Man page
|
| getImgAnnIds |
Man page
Source code
|
| getImgAnnOutlineDf |
Man page
Source code
|
| getImgAnnRange |
Man page
Source code
|
| getImgAnnSf |
Man page
Source code
|
| getImgAnnSummaryDf |
Man page
Source code
|
| getImgAnnTags |
Man page
Source code
|
| getInitiationInfo |
Man page
Source code
|
| getInitiationInput |
Man page
Source code
|
| getMatrices |
Man page
Source code
|
| getMatrix |
Man page
Source code
|
| getMethod |
Source code
|
| getMethodName |
Source code
|
| getMethodUnit |
Source code
|
| getModelEvaluationDf |
Man page
|
| getModelEvaluationDf,ImageAnnotationScreening-method |
Man page
|
| getModelEvaluationDf,SpatialTrajectoryScreening-method |
Man page
|
| getOutlineVarName |
Man page
Source code
|
| getPatternNames |
Man page
Source code
|
| getPcaDf |
Man page
Source code
|
| getPcaMtr |
Man page
Source code
|
| getPixelDf |
Man page
Source code
|
| getPixelScaleFactor |
Man page
|
| getPrResults |
Man page
Source code
|
| getProjectionDf |
Man page
|
| getPubExample |
Man page
Source code
|
| getResultsDf |
Man page
|
| getResultsDf,ImageAnnotationScreening-method |
Man page
|
| getResultsDf,SpatialTrajectoryScreening-method |
Man page
|
| getResultsVec |
Man page
|
| getResultsVec,ImageAnnotationScreening-method |
Man page
|
| getResultsVec,SpatialTrajectoryScreening-method |
Man page
|
| getSampleAreaSize |
Man page
|
| getSampleName |
Man page
|
| getSampleNames |
Man page
Source code
|
| getSegmentDf |
Man page
Source code
|
| getSegmentNames |
Man page
Source code
|
| getSegmentationNames |
Man page
|
| getSegmentationVariableNames |
Man page
|
| getSignatureEnrichment |
Man page
|
| getSmrdResultsDf |
Man page
|
| getSpCorCluster |
Man page
Source code
|
| getSpCorClusterNames |
Man page
Source code
|
| getSpCorResults |
Man page
Source code
|
| getSparkxGeneDf |
Man page
|
| getSparkxGenes |
Man page
|
| getSparkxResults |
Man page
|
| getSpataDf |
Man page
|
| getSpataDir |
Man page
|
| getSpatialMethod |
Man page
Source code
|
| getSpatialTrajectories |
Man page
|
| getSpatialTrajectory |
Man page
|
| getSpatialTrajectoryIds |
Man page
|
| getStsDf |
Man page
|
| getTissueOutlineDf |
Man page
|
| getTrajectoryDf |
Man page
|
| getTrajectoryIds |
Man page
|
| getTrajectoryLength |
Man page
|
| getTrajectoryNames |
Man page
Source code
|
| getTrajectoryScreeningDf |
Man page
Source code
|
| getTrajectorySegmentDf |
Man page
|
| getTsneDf |
Man page
|
| getUmapDf |
Man page
|
| getVariableNames |
Man page
|
| get_img_ann_helper |
Man page
Source code
|
| ggpInit |
Man page
Source code
|
| ggpLayerAxesClean |
Man page
Source code
|
| ggpLayerAxesSI |
Man page
Source code
|
| ggpLayerColorGroupScale |
Man page
Source code
|
| ggpLayerEncirclingGroups |
Source code
|
| ggpLayerEncirclingIAS |
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
|
| ggpLayerGroupOutline |
Man page
Source code
|
| ggpLayerHorizonIAS |
Man page
Source code
|
| ggpLayerImage |
Man page
Source code
|
| ggpLayerImageAnnotation |
Source code
|
| ggpLayerImgAnnBorder |
Man page
Source code
|
| ggpLayerImgAnnOutline |
Man page
Source code
|
| ggpLayerImgAnnPointer |
Man page
Source code
|
| ggpLayerImgAnnRect |
Man page
Source code
|
| ggpLayerLineplotAid |
Man page
Source code
|
| ggpLayerRect |
Man page
Source code
|
| ggpLayerSampleMask |
Source code
|
| ggpLayerScaleBarSI |
Man page
Source code
|
| ggpLayerThemeCoords |
Man page
Source code
|
| ggpLayerTissueOutline |
Man page
Source code
|
| ggpLayerTrajectories |
Man page
Source code
|
| ggpLayerZoom |
Man page
Source code
|
| ggpLayer_dummy |
Man page
Source code
|
| ggplot_dummy |
Man page
Source code
|
| ggplot_family |
Man page
Source code
|
| gradientToModelIAS |
Man page
Source code
|
| gradientToModelSTS |
Man page
Source code
|
| gsdf |
Man page
|
| hide_unit |
Source code
|
| hlpr_add_barcode_suffix |
Man page
Source code
|
| hlpr_add_models |
Source code
Source code
|
| hlpr_add_old_coords |
Man page
Source code
|
| hlpr_add_residuals |
Source code
|
| hlpr_add_residuals2 |
Source code
|
| hlpr_add_residuals_customized |
Source code
|
| hlpr_add_residuals_diet |
Source code
|
| hlpr_adjust_legend_size |
Man page
Source code
|
| hlpr_assess_trajectory_trends |
Source code
|
| hlpr_assess_trajectory_trends_customized |
Source code
|
| hlpr_assign_arguments |
Man page
Source code
|
| hlpr_breaks |
Man page
Source code
|
| hlpr_compare_samples |
Man page
Source code
|
| hlpr_display_subtitle |
Source code
|
| hlpr_display_title |
Source code
|
| hlpr_dist_mtr_to_df |
Man page
Source code
|
| hlpr_drop_all_na |
Source code
|
| hlpr_filter_trend |
Source code
|
| hlpr_gene_set_name |
Man page
Source code
|
| hlpr_geom_trajectory_fit |
Man page
Source code
|
| hlpr_image_add_on |
Man page
Source code
|
| hlpr_image_add_on2 |
Source code
|
| hlpr_image_to_df |
Source code
|
| hlpr_join_with_color_by |
Man page
Source code
|
| hlpr_labs_add_on |
Man page
Source code
|
| hlpr_name_models |
Source code
|
| hlpr_normalize_imap |
Man page
Source code
|
| hlpr_normalize_vctr |
Man page
Source code
|
| hlpr_one_distinct |
Man page
Source code
|
| hlpr_process_spatial_correlation_cluster |
Man page
Source code
|
| hlpr_rank_trajectory_trends |
Man page
Source code
|
| hlpr_rank_trajectory_trends_customized |
Source code
|
| hlpr_run_cnva_pca |
Source code
|
| hlpr_save_spata_object |
Man page
Source code
|
| hlpr_scatterplot |
Man page
Source code
|
| hlpr_smooth |
Man page
Source code
|
| hlpr_smooth_shiny |
Man page
Source code
|
| hlpr_subset_across |
Man page
Source code
|
| hlpr_summarize_residuals |
Source code
|
| hlpr_summarize_trajectory_df |
Man page
Source code
|
| hlpr_transfer_slot_content |
Source code
|
| hlpr_vector_projection |
Man page
Source code
|
| hlpr_widen_trajectory_df |
Man page
Source code
|
| identifyTissueOutline |
Man page
Source code
|
| identifyTissueSections |
Man page
Source code
|
| imageAnnotationScreening |
Man page
Source code
|
| imageAnnotationToSegmentation |
Man page
Source code
|
| image_annotations |
Man page
|
| image_dummy |
Man page
Source code
|
| img_ann_highlight_group_button |
Source code
|
| include_tissue_outline |
Man page
Source code
|
| incorporate_tissue_outline |
Source code
|
| inferSingleCellGradient |
Man page
Source code
|
| initiateSpataObject_10X |
Man page
Source code
|
| initiateSpataObject_CountMtr |
Man page
Source code
|
| initiateSpataObject_Empty |
Man page
Source code
|
| initiateSpataObject_Examples |
Man page
Source code
|
| initiateSpataObject_ExprMtr |
Man page
Source code
|
| initiateSpataObject_Visium |
Source code
|
| intersect_polygons |
Man page
Source code
|
| isDirToSpaceRangerOutput |
Source code
|
| isFeature |
Source code
|
| isFlipped |
Source code
|
| isGene |
Source code
|
| isGeneSet |
Source code
|
| isNumericVariable |
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_eUOL_dist |
Source code
|
| is_exclam |
Source code
|
| is_image_dir |
Source code
|
| is_number |
Source code
|
| is_numeric_input |
Source code
|
| is_percentage |
Source code
|
| is_pixel_dist |
Source code
|
| is_spatial_measure |
Source code
|
| is_subsetted_by_segment |
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
|
| lastImageAnnotation |
Source code
|
| legendBottom |
Man page
|
| legendColor |
Man page
Source code
|
| legendLeft |
Man page
|
| legendNone |
Man page
|
| legendRight |
Man page
|
| legendTop |
Man page
|
| loadCorrespondingCDS |
Source code
|
| loadCorrespondingSeuratObject |
Source code
|
| loadGSDF |
Man page
Source code
|
| loadGeneSetDf |
Man page
|
| loadImage |
Man page
Source code
|
| loadImageDefault |
Man page
Source code
|
| loadImageHighres |
Man page
Source code
|
| loadImageLowres |
Man page
Source code
|
| 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_pretty_model_names |
Source code
|
| make_scattermore_add_on |
Source code
|
| mapImageAnnotationTags |
Man page
Source code
|
| mergeGroups |
Man page
Source code
|
| mergeSpataObjects |
Source code
|
| mergeTissueSections |
Man page
Source code
|
| method_hclust |
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 |
Man page
Source code
|
| nCounts |
Man page
Source code
|
| nGenes |
Man page
Source code
|
| nImageAnnotations |
Man page
Source code
|
| nImageDims |
Source code
|
| nSpatialTrajectories |
Man page
Source code
|
| nTrajectories |
Man page
Source code
|
| nest_shifted_projection_df |
Source code
|
| normalize |
Man page
|
| normalize_smrd_projection_df |
Source code
|
| numericSlider |
Source code
|
| object_dummy |
Man page
Source code
|
| order_df |
Source code
|
| pb_dummy |
Man page
Source code
|
| pheatmap |
Man page
Source code
|
| pick_vars |
Source code
|
| plotAutoencoderAssessment |
Man page
Source code
|
| plotAutoencoderResults |
Man page
Source code
|
| plotBarchart |
Man page
Source code
|
| plotBoxplot |
Man page
Source code
|
| plotClockplot |
Man page
|
| plotClockplot,ImageAnnotationScreening-method |
Man page
|
| plotClockplot,spata2-method |
Man page
|
| plotCnvHeatmap |
Man page
Source code
|
| plotCnvLineplot |
Man page
Source code
|
| plotCustomizedTrajectoryTrends |
Source code
|
| plotDeaDotPlot |
Man page
Source code
|
| plotDeaGeneCount |
Man page
Source code
|
| plotDeaHeatmap |
Man page
Source code
|
| plotDeaLogFC |
Man page
Source code
|
| plotDeaPvalues |
Man page
Source code
|
| plotDeaSummary |
Man page
Source code
|
| plotDeaVolcano |
Man page
Source code
|
| plotDeaVolcano1v1 |
Man page
Source code
|
| plotDendrogram |
Man page
Source code
|
| plotDendrogramCnv |
Source code
|
| plotDensityplot |
Man page
|
| plotDistribution |
Source code
|
| plotDistribution2 |
Source code
|
| plotDistributionAcross |
Source code
|
| plotDistributionAcross2 |
Source code
|
| plotDistributionDiscrete |
Source code
|
| plotFourStates |
Man page
Source code
|
| plotFourStates2 |
Man page
Source code
|
| plotGeneDendrogram |
Man page
Source code
|
| plotGseaDotPlot |
Man page
Source code
|
| plotHistogram |
Man page
Source code
|
| plotIasBarplot |
Man page
Source code
|
| plotIasBarplotSC |
Man page
Source code
|
| plotIasEvaluation |
Man page
Source code
|
| plotIasHeatmap |
Man page
Source code
|
| plotIasLineplot |
Man page
Source code
|
| plotIasLineplotFitted |
Man page
Source code
|
| plotIasLineplotSC |
Man page
Source code
|
| plotIasRidgeplot |
Man page
Source code
|
| plotIasRidgeplotSC |
Man page
Source code
|
| plotImage |
Man page
Source code
|
| plotImageAnnotations |
Man page
Source code
|
| plotImageGgplot |
Man page
|
| plotImagesGgplot |
Man page
|
| plotMosaicplot |
Man page
|
| plotOverview |
Man page
|
| plotOverview,ImageAnnotationScreening-method |
Man page
|
| plotOverview,SpatialTrajectoryScreening-method |
Man page
|
| plotPca |
Man page
Source code
|
| plotPcaVariation |
Man page
Source code
|
| plotPseudotime |
Man page
Source code
|
| plotRidgeplot |
Man page
Source code
|
| plotRiverplot |
Man page
Source code
|
| plotScatterplot |
Man page
Source code
|
| plotSegmentation |
Source code
|
| plotSpatialTrajectories |
Man page
Source code
|
| plotStatisticsInteractive |
Man page
Source code
|
| plotSurface |
Man page
|
| plotSurface,data.frame-method |
Man page
|
| plotSurface,spata2-method |
Man page
|
| plotSurface2 |
Source code
|
| plotSurfaceAverage |
Man page
|
| plotSurfaceBase |
Man page
|
| plotSurfaceComparison |
Man page
|
| plotSurfaceComparison2 |
Man page
|
| plotSurfaceIAS |
Man page
|
| plotSurfaceIAS,ImageAnnotationScreening-method |
Man page
|
| plotSurfaceIAS,spata2-method |
Man page
|
| plotSurfaceInteractive |
Man page
|
| plotSurfaceOutline |
Source code
|
| plotSurfaceQuantiles |
Man page
|
| plotSurfaceSC |
Man page
|
| plotTrajectory |
Man page
Source code
|
| plotTrajectoryBarplot |
Man page
Source code
|
| plotTrajectoryEvaluation |
Man page
Source code
|
| plotTrajectoryFeatures |
Source code
|
| plotTrajectoryFeaturesDiscrete |
Source code
|
| plotTrajectoryFit |
Source code
|
| plotTrajectoryGeneSets |
Source code
|
| plotTrajectoryGenes |
Source code
|
| plotTrajectoryHeatmap |
Man page
Source code
|
| plotTrajectoryLineplot |
Man page
Source code
|
| plotTrajectoryLineplotFitted |
Man page
Source code
|
| plotTrajectoryRidgeplot |
Man page
Source code
|
| plotTsne |
Man page
Source code
|
| plotTsneComparison |
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,ImageAnnotationScreening-method |
Man page
|
| plotVolcano,SpatialTrajectoryScreening-method |
Man page
|
| plot_overview |
Source code
|
| plot_screening_evaluation |
Man page
Source code
|
| plot_type_dummy |
Man page
Source code
|
| printAutoencoderSummary |
Man page
Source code
|
| printDeaOverview |
Man page
Source code
|
| printDefaultInstructions |
Man page
Source code
|
| printGeneSetOverview |
Man page
Source code
|
| print_family |
Man page
Source code
|
| process_angle_justification |
Source code
|
| process_axis |
Source code
|
| process_expand_input |
Man page
Source code
|
| process_ranges |
Man page
Source code
|
| process_sce_bayes_space |
Source code
|
| process_seurat_object |
Man page
Source code
|
| project_on_trajectory |
Man page
Source code
|
| project_on_vector |
Man page
Source code
|
| pull_slot |
Source code
|
| reduce_vec |
Man page
Source code
|
| relateToImageAnnotation |
Man page
Source code
|
| relevelGroups |
Man page
Source code
|
| removeAnnotation |
Man page
Source code
|
| renameFeatures |
Man page
Source code
|
| renameGroups |
Man page
Source code
|
| renameImgAnn |
Man page
Source code
|
| renameSegments |
Man page
Source code
|
| resetImageJustification |
Man page
Source code
|
| resizingSegmentsGrob |
Man page
Source code
|
| resizingTextGrob |
Man page
Source code
|
| rm_na |
Source code
|
| rotateAll |
Man page
Source code
|
| rotateCoordinates |
Man page
Source code
|
| rotateCoordsDf |
Man page
Source code
|
| rotateImage |
Man page
Source code
|
| rotateImageAnnotations |
Man page
Source code
|
| rotateSpatialTrajectories |
Man page
Source code
|
| rotate_coord |
Source code
|
| rotate_coords_df |
Man page
Source code
|
| runAutoencoderAssessment |
Man page
Source code
|
| runAutoencoderDenoising |
Man page
Source code
|
| runBayesSpaceClustering |
Man page
Source code
|
| runCnvAnalysis |
Man page
|
| runDEA |
Man page
|
| runDeAnalysis |
Man page
|
| runGSEA |
Man page
|
| runPca |
Man page
|
| runPca2 |
Man page
|
| runSeuratClustering |
Man page
|
| runSparkx |
Man page
|
| runSpatialCorrelationAnalysis |
Man page
Source code
|
| runTsne |
Man page
|
| runTsne2 |
Man page
|
| runUmap |
Man page
|
| runUmap2 |
Man page
|
| sample_name |
Man page
Source code
|
| saveCorrespondingCDS |
Man page
Source code
|
| saveCorrespondingSeuratObject |
Man page
Source code
|
| saveGeneSetDf |
Man page
Source code
|
| saveSpataObject |
Man page
Source code
|
| sc_deconvolution |
Man page
|
| scaleAll |
Man page
Source code
|
| scaleCoordinates |
Man page
Source code
|
| scaleCoordsDf |
Man page
Source code
|
| scaleImage |
Man page
Source code
|
| scaleImageAnnotations |
Man page
Source code
|
| scaleSpatialTrajectories |
Man page
Source code
|
| scale_color_add_on |
Man page
|
| scale_coords_df |
Man page
Source code
|
| scale_factors |
Man page
|
| scale_nuclei_df |
Source code
|
| section_dummy |
Man page
Source code
|
| setActiveExpressionMatrix |
Man page
Source code
|
| setActiveMatrix |
Man page
Source code
|
| setAutoencoderAssessment |
Man page
Source code
|
| setBarcodes |
Man page
Source code
|
| setCCD |
Man page
Source code
|
| setCnvResults |
Man page
Source code
|
| setCoordsDf |
Man page
Source code
|
| setCountMatrix |
Man page
Source code
|
| setDeaResultsDf |
Source code
|
| setDefault |
Man page
Source code
|
| setDefaultGrouping |
Man page
Source code
|
| setDefaultInstructions |
Man page
Source code
|
| setDefaultTrajectory |
Man page
Source code
|
| setDefaultTrajectoryId |
Man page
|
| setDenoisedMatrix |
Man page
Source code
|
| setDirectoryInstructions |
Man page
Source code
|
| setFeatureDf |
Man page
Source code
|
| setGeneSetDf |
Man page
Source code
|
| setImage |
Source code
|
| setImageAnnotation |
Man page
Source code
|
| setImageAnnotations |
Man page
Source code
|
| setImageDirDefault |
Man page
Source code
|
| setImageDirHighres |
Man page
Source code
|
| setImageDirLowres |
Man page
Source code
|
| setImageObject |
Man page
Source code
|
| setImageOrigin |
Man page
Source code
|
| setInitiationInfo |
Man page
Source code
|
| setNormalizedMatrix |
Man page
Source code
|
| setOutlineVarName |
Man page
Source code
|
| setPcaDf |
Man page
Source code
|
| setPixelScaleFactor |
Man page
Source code
|
| setPrResults |
Man page
Source code
|
| setScaledMatrix |
Man page
Source code
|
| setSpCorResults |
Man page
Source code
|
| setSpataDir |
Man page
Source code
|
| setSpatialMethod |
Man page
Source code
|
| setSpatialMethodInfo |
Man page
Source code
|
| setSpatialMethodSlot |
Man page
Source code
|
| setTissueOutline |
Man page
Source code
|
| setTrajectories |
Man page
Source code
|
| setTrajectory |
Man page
Source code
|
| setTsneDf |
Man page
Source code
|
| setUmapDf |
Man page
Source code
|
| set_dummy |
Man page
Source code
|
| seurat_object_dummy |
Man page
Source code
|
| shiftTrajectoryDf |
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
|
| 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
|
| smoothSpatially |
Man page
Source code
|
| spata2 |
Man page
|
| spata2-class |
Man page
|
| spatialTrajectoryScreening |
Man page
Source code
|
| spatial_segmentations |
Man page
|
| spatial_trajectories |
Man page
|
| spatial_trajectory |
Man page
|
| spatial_trajectory-class |
Man page
|
| splitHorizontally |
Source code
|
| strongH3 |
Source code
|
| strongH5 |
Source code
|
| subsetByBarcodes |
Man page
Source code
|
| subsetByBarcodes_CountMtr |
Source code
|
| subsetByBarcodes_ExprMtr |
Source code
|
| subsetByGenes |
Man page
|
| subsetBySegment_CountMtr |
Source code
|
| subsetBySegment_ExprMtr |
Source code
|
| subsetIAS |
Man page
|
| summarizeIAS |
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
|
| textInputWrapper |
Source code
|
| theme_lineplot_gradient |
Man page
Source code
|
| theme_ridgeplot_gradient |
Man page
Source code
|
| theme_trajectory_fit |
Man page
Source code
|
| tissueOutlineIdentified |
Man page
Source code
|
| tissueSectionsIdentfied |
Man page
Source code
|
| transfer_slot_content |
Man page
Source code
|
| transformSeuratToSpata |
Man page
Source code
|
| transformSpataToCDS |
Man page
Source code
|
| transformSpataToSeurat |
Man page
Source code
|
| transform_area_si_to_pixel |
Man page
Source code
|
| transform_area_si_to_pixels |
Man page
Source code
|
| transform_dist_si_to_pixel |
Man page
Source code
|
| transform_dist_si_to_pixels |
Man page
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
|
| updateSpataObject |
Man page
Source code
|
| update_dummy |
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
|
| validDeAnalysisMethods |
Man page
Source code
|
| validDefaultInstructionSlots |
Man page
Source code
|
| validDimRedMethods |
Man page
Source code
|
| validDirectoryInstructionSlots |
Man page
Source code
|
| validDistanceMethods |
Man page
Source code
|
| validEuropeanUnitsOfLength |
Man page
Source code
|
| validHierarchicalClusterMethods |
Man page
Source code
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| validImageClasses |
Man page
Source code
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| validModelNames |
Man page
Source code
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| validPadjMethods |
Man page
Source code
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| validPatternRecognitionMethods |
Man page
Source code
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| validPlotTypes |
Man page
Source code
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| validPubExamples |
Man page
Source code
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| validSpatialMethods |
Man page
Source code
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| validTrajectoryTrends |
Man page
Source code
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| validUnits |
Man page
Source code
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| validUnitsOfArea |
Man page
Source code
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| validUnitsOfAreaSI |
Man page
Source code
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| validUnitsOfLength |
Man page
Source code
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| validUnitsOfLengthSI |
Man page
Source code
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| validateSpataObject |
Source code
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| validate_only_one_arg_specified |
Source code
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| validation |
Man page
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| variable |
Man page
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| variable_num |
Man page
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| variables_num |
Man page
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| version_string |
Source code
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| visium_coords |
Man page
|
| vselect |
Man page
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| waive_if_null |
Source code
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| whichSpaceRangerVersion |
Source code
|
