API for kueckelj/SPATA
A Toolbox for Spatial Gene Expression Analysis
| Global functions | |
|---|---|
| across | Man page Source code |
| addFeatures | Man page Source code |
| addGeneSet | Man page Source code |
| addGeneSetsInteractive | Man page Source code |
| addTsneData | Man page Source code |
| addUmapData | Man page Source code |
| adjustGeneSetDf | Man page Source code |
| adjusting_check_dummy | Man page Source code |
| all_colorpanels | Man page |
| all_colorspectra | Man page |
| assessTrajectoryTrends | Man page Source code |
| assessTrajectoryTrends2 | Man page Source code |
| average_genes | Man page Source code |
| check_assign | Man page Source code |
| check_atdf | Man page 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_de_df | Man page Source code |
| check_display | Man page 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_method | Man page Source code |
| check_monocle_input | Man page Source code |
| check_object | Man page Source code |
| check_pt | Man page Source code |
| check_rtdf | Man page Source code |
| check_sample | 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_stdf | Man page Source code |
| check_summarized_trajectory_df | Man page Source code |
| check_trajectory | 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 |
| clrp | Man page Source code |
| compileCellDataSet | Man page Source code |
| compileSeuratObject | Man page Source code |
| coordinates | Man page |
| coordinates,spata-method | Man page |
| coordinates<- | Man page |
| coordinates<-,spata-method | Man page |
| countMtr | Man page |
| countMtr,spata-method | Man page |
| createSegmentation | Man page Source code |
| createTrajectories | Man page Source code |
| ctdf | Man page |
| ctdf,spatial_trajectory-method | Man page |
| data_counts | Man page |
| data_counts-class | Man page |
| dim_red | Man page |
| dim_red-class | Man page |
| discardGeneSets | Man page Source code |
| examineClusterResults | Man page Source code |
| examineDeResults | Man page Source code |
| examineTrajectoryAssessment | Man page Source code |
| exprMtr | Man page |
| exprMtr,spata-method | Man page |
| featureData | Man page |
| featureData,spata-method | Man page |
| featureData<- | Man page |
| featureData<-,spata-method | Man page |
| filterDE | Man page Source code |
| filterTrends | Man page Source code |
| findDE | Man page Source code |
| findMonocleClusters | Man page Source code |
| getBarcodes | Man page Source code |
| getC_joinW_combo | Man page Source code |
| getCoordinates | Man page Source code |
| getCoordinatesSegment | Man page Source code |
| getCountMatrix | Man page Source code |
| getDimRedData | Man page Source code |
| getExpressionMatrix | Man page Source code |
| getFeatureData | Man page Source code |
| getFeatureNames | Man page Source code |
| getFeatureValues | Man page Source code |
| getFeatureVariables | 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 |
| getSegmentNames | Man page Source code |
| getSpataDf | Man page Source code |
| getTrajectoryComment | Man page |
| getTrajectoryComment,spata-method | Man page |
| getTrajectoryComment,spatial_trajectory-method | Man page |
| getTrajectoryDf | Man page Source code |
| getTrajectoryNames | Man page Source code |
| getTrajectoryObject | Man page Source code |
| getTsneData | Man page Source code |
| getUmapData | Man page Source code |
| gsdf | Man page |
| hlpr_add_models | Man page Source code |
| hlpr_add_residuals | Man page Source code |
| hlpr_assess_trajectory_trends | Man page Source code |
| hlpr_assign | Man page Source code |
| hlpr_compare_samples | Man page Source code |
| hlpr_compile_trajectory | Man page Source code |
| hlpr_filter_trend | Man page Source code |
| hlpr_gene_set_name | Man page Source code |
| hlpr_image_add_on | Man page Source code |
| hlpr_image_add_on2 | Man page Source code |
| hlpr_labs_add_on | Man page Source code |
| hlpr_name_models | Man page Source code |
| hlpr_normalize_imap | Man page Source code |
| hlpr_normalize_vctr | Man page Source code |
| hlpr_one_distinct | Man page Source code |
| hlpr_rank_trajectory_trends | 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 | Man page Source code |
| hlpr_summarize_trajectory_df | Man page Source code |
| hlpr_vector_projection | Man page Source code |
| hlpr_widen_trajectory_df | Man page Source code |
| image | Man page |
| image,spata-method | Man page |
| image_dummy | Man page Source code |
| initiateSpataObject_10X | Man page Source code |
| joinWith | Man page Source code |
| joinWithFeatures | Man page Source code |
| joinWithGeneSets | Man page Source code |
| joinWithGenes | Man page Source code |
| joinWithVariables | Man page Source code |
| lazy_check_dummy | Man page Source code |
| loadSpataObject | Man page Source code |
| moduleAddGeneSetsServer | Man page Source code |
| moduleAddGeneSetsUI | Man page Source code |
| moduleSurfacePlotServer | Man page Source code |
| moduleSurfacePlotUI | Man page Source code |
| normalize | Man page Source code |
| pheatmap | Man page Source code |
| plotDeHeatmap | Man page Source code |
| plotDimRed | Source code |
| plotDistribution | Man page Source code |
| plotDistribution2 | Man page Source code |
| plotDistributionAcross | Man page Source code |
| plotDistributionAcross2 | Man page Source code |
| plotDistributionDiscrete | Man page Source code |
| plotFourStates | Man page Source code |
| plotFourStates2 | Man page Source code |
| plotPseudotime | Man page Source code |
| plotSegmentation | Man page Source code |
| plotSurface | Man page Source code |
| plotSurface2 | Man page Source code |
| plotSurfaceComparison | Man page Source code |
| plotSurfaceComparison2 | Man page Source code |
| plotSurfaceInteractive | Man page Source code |
| plotTSNE | Man page Source code |
| plotTrajectory | Man page Source code |
| plotTrajectoryFeatures | Man page Source code |
| plotTrajectoryFeaturesDiscrete | Man page Source code |
| plotTrajectoryFit | Man page Source code |
| plotTrajectoryGeneSets | Man page Source code |
| plotTrajectoryGenes | Man page Source code |
| plotTrajectoryHeatmap | Man page Source code |
| plotUMAP | Man page Source code |
| plot_family | Man page Source code |
| samples | Man page |
| samples,spata-method | Man page |
| saveGeneSetDf | Man page Source code |
| saveSpataObject | Man page Source code |
| scale_color_add_on | Man page |
| spata | Man page |
| spata-class | Man page |
| spata_version | Man page |
| spatial_trajectory | Man page |
| spatial_trajectory-class | Man page |
| subsetSpataObject | Man page Source code |
| tab_create_segmentation_return | Man page Source code |
| tab_create_trajectories_return | Man page Source code |
| tab_surface_plots_app | Man page Source code |
| tab_surface_plots_return | Man page Source code |
| trajectory | Man page |
| trajectory,spata-method | Man page |
| trajectory_patterns | Man page |
| validateSpataObject | Man page Source code |
| validation | Man page Source code |
| variable | Man page Source code |
| variables_num | Man page Source code |
| verbose | Man page Source code |
