Files in jbergenstrahle/STUtility

Analysis and visualization of Spatial Transcriptomics data

R/2D_point_pattern.R R/3D_viusalization.R R/HSVencoding.R R/Image_resolution_switch.R R/Mask_functions.R R/QC.R R/RegionNeighbours.R R/Rigid_transformation.R R/RunNMF.R R/Spatial_genes.R R/Staffli.R R/Visualization.R R/Visualization_utilities.R R/crop_utilities.R R/facet_grid_SC.R R/generics.R R/image_processing.R R/image_processing_utilities.R R/manual_annotation.R R/pre_processing.R R/process_from_table.R R/utilities.R README.md man/AlignImages.Rd man/ColorBlender.Rd man/ConvertGeneNames.Rd man/CorSpatialDims.Rd man/CorSpatialGenes.Rd man/Create3DStack.Rd man/CreateStaffliObject.Rd man/Create_annotation.Rd man/CropImages.Rd man/CustomFacetWrap.Rd man/DimOverlay.Rd man/DimPlot3D.Rd man/EdgeMask.Rd man/FactorGeneLoadingPlot.Rd man/FeatureOverlay.Rd man/FeaturePlot3D.Rd man/FilterObjects.Rd man/GetCoords.Rd man/GetCropWindows.Rd man/GetSpatNet.Rd man/GetStaffli.Rd man/HSVOverlay.Rd man/HSVPlot.Rd man/HSVPlot3D.Rd man/ImagePlot.Rd man/InputFromTable.Rd man/LoadImages.Rd man/ManualAlignImages.Rd man/ManualAnnotation.Rd man/MaskImages.Rd man/MergeSTData.Rd man/Merger.Rd man/RegionNeighbours.Rd man/RunNMF.Rd man/ST.DimPlot.Rd man/ST.FeaturePlot.Rd man/ST.ImagePlot.Rd man/ST.rgbDimPlot.Rd man/STPlot.Rd man/STutility-package.Rd man/SetQuantile.Rd man/SmoothPlot.Rd man/Staffli-class.Rd man/Staffli-get-methods.Rd man/Staffli-set-methods.Rd man/SubsetSTData.Rd man/SummarizeAssocFeatures.Rd man/SwitchResolution.Rd man/Warp.Rd man/WarpImages.Rd man/add.margins.Rd man/apply.transform.Rd man/combine.tr.Rd man/create.array.from.feature.vals.Rd man/create.cols.from.array.Rd man/cscale.Rd man/dark_theme.Rd man/draw_scalebar.Rd man/facet_wrap_custom.Rd man/feature.scaler.Rd man/find.optimal.transform.Rd man/g_legend.Rd man/generate.map.affine.Rd man/generate.map.rot.Rd man/get.edges.Rd man/get.edges.Seurat.Rd man/get.edges.Staffli.Rd man/getExtension.Rd man/grid.from.staffli.Rd man/ica_init.Rd man/icpmat.Rd man/iminfo.Rd man/interpolate_2D_data.Rd man/labelRGB.Rd man/make.plot.Rd man/mirror.Rd man/names.Rd man/obtain.array.coords.Rd man/palette.select.Rd man/parse.spot.file.Rd man/plot.Rd man/prep.sb.Rd man/qc.scatter.Rd man/qcGenes.Rd man/qcSamples.Rd man/qcSpots.Rd man/rasterize_scatter.Rd man/rasterlists.Rd man/rigid.refl.Rd man/rigid.rot.Rd man/rigid.stretch.Rd man/rigid.transf.Rd man/rigid.transl.Rd man/rnmf.Rd man/rotate.Rd man/samplenames.Rd man/scale_override.Rd man/scaled.imdims.Rd man/scatter_HE.Rd man/show.Rd man/sleepy.Rd man/slic.Rd man/spatial_dim_plot.Rd man/spatial_feature_plot.Rd man/spatial_hsv_plot.Rd man/st.load.matrix.Rd man/stretch.Rd man/translate.Rd