Files in kueckelj/SPATA
A Toolbox for Spatial Gene Expression Analysis

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/S4-documentation.R R/S4-generic-functions.R R/add-family.R R/check-family-adjusting.R R/check-family-lazy.R R/check-family-validation.R R/checkpoint.R R/compile-family.R R/create_family.R R/data.R R/documentation-dummies.R R/gene-expression-analysis.R R/genes-and-gene-sets.R R/get-family.R R/helper-functions.R R/imported-functions.R R/intern-analysis.R R/joinWith-family.R R/loading-and-saving.R R/miscellaneous-helper-functions.R R/module-add-gene-sets.R R/module-surface-plot.R R/package-dependencies.R R/plot-family-miscellaneous.R R/plot-family-surface.R R/plot-family-trajectory.R R/shiny-dashboard-tab-items.R R/spata-object-manipulation.R R/trajectory-analysis.R R/validation.R README.md

SPATA.Rproj

data/gsdf.rda

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man/across.Rd man/addFeatures.Rd man/addGeneSet.Rd man/addUmapData.Rd man/adjustGeneSetDf.Rd man/adjusting_check_dummy.Rd man/all_colorpanels.Rd man/assessTrajectoryTrends.Rd man/average_genes.Rd man/check_assign.Rd man/check_atdf.Rd man/check_color_to.Rd man/check_compiled_trajectory_df.Rd man/check_coordinate_variables.Rd man/check_coords_df.Rd man/check_de_df.Rd man/check_display.Rd man/check_feature_df.Rd man/check_features.Rd man/check_gene_sets.Rd man/check_genes.Rd man/check_method.Rd man/check_monocle_input.Rd man/check_object.Rd man/check_pt.Rd man/check_sample.Rd man/check_segment.Rd man/check_slot_coordinates.Rd man/check_smooth.Rd man/check_spata_df.Rd man/check_stdf.Rd man/check_summarized_trajectory_df.Rd man/check_trajectory.Rd man/check_uniform_genes.Rd man/check_variables.Rd man/checkpoint.Rd man/clrp.Rd man/compileCellDataSet.Rd man/compileSeuratObject.Rd man/createSegmentation.Rd man/createTrajectories.Rd man/data_counts-class.Rd man/dim_red-class.Rd man/discardGeneSets.Rd man/examineClusterResults.Rd man/examineDeResults.Rd man/examineTrajectoryAssessment.Rd man/filterDE.Rd man/filterTrends.Rd man/findDE.Rd man/findMonocleClusters.Rd man/getBarcodes.Rd man/getC_joinW_combo.Rd man/getCoordinates.Rd man/getDimRedData.Rd man/getExpressionMatrix.Rd man/getFeatureData.Rd man/getFeatureNames.Rd man/getFeatureValues.Rd man/getFeatureVariables.Rd man/getGeneSetOverview.Rd man/getGeneSets.Rd man/getGenes.Rd man/getSegmentNames.Rd man/getSpataDf.Rd man/getTrajectoryComment-spata-method.Rd man/getTrajectoryComment.Rd man/getTrajectoryDf.Rd man/getTrajectoryNames.Rd man/getTrajectoryObject.Rd man/gsdf.Rd man/hlpr_add_models.Rd man/hlpr_assess_trajectory_trends.Rd man/hlpr_assign.Rd man/hlpr_compare_samples.Rd man/hlpr_compile_trajectory.Rd man/hlpr_gene_set_name.Rd man/hlpr_image_add_on.Rd man/hlpr_labs_add_on.Rd man/hlpr_normalize_imap.Rd man/hlpr_normalize_vctr.Rd man/hlpr_one_distinct.Rd man/hlpr_rank_trajectory_trends.Rd man/hlpr_smooth.Rd man/hlpr_smooth_shiny.Rd man/hlpr_subset_across.Rd man/hlpr_summarize_trajectory_df.Rd man/hlpr_vector_projection.Rd man/hlpr_widen_trajectory_df.Rd man/image-spata-method.Rd man/image.Rd man/image_dummy.Rd man/initiateSpataObject_10X.Rd man/joinWith.Rd man/lazy_check_dummy.Rd man/loadSpataObject.Rd man/moduleAddGeneSetsServer.Rd man/moduleAddGeneSetsUI.Rd man/moduleSurfacePlotServer.Rd man/moduleSurfacePlotUI.Rd man/normalize.Rd man/pheatmap.Rd man/plotDeHeatmap.Rd man/plotDistribution.Rd man/plotDistributionAcross.Rd man/plotDistributionDiscrete.Rd man/plotFourStates.Rd man/plotPseudotime.Rd man/plotSegmentation.Rd man/plotSurface.Rd man/plotSurfaceComparison.Rd man/plotTrajectory.Rd man/plotTrajectoryFeatures.Rd man/plotTrajectoryFit.Rd man/plotTrajectoryHeatmap.Rd man/plotUMAP.Rd man/plot_family.Rd man/saveGeneSetDf.Rd man/scale_color_add_on.Rd man/spata-class.Rd man/spata_version.Rd man/spatial_trajectory-class.Rd man/subsetSpataObject.Rd man/tab_create_segmentation_return.Rd man/tab_create_trajectories_return.Rd man/tab_surface_plots_app.Rd man/tab_surface_plots_return.Rd man/trajectory_patterns.Rd man/validateSpataObject.Rd man/validation.Rd man/variable.Rd man/variables_num.Rd man/verbose.Rd

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.

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kueckelj/SPATA
A Toolbox for Spatial Gene Expression Analysis

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A Toolbox for Spatial Gene Expression Analysis

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kueckelj/SPATA A Toolbox for Spatial Gene Expression Analysis

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kueckelj/SPATA
A Toolbox for Spatial Gene Expression Analysis

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A Toolbox for Spatial Gene Expression Analysis