├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── 2D_point_pattern.R ├── 3D_viusalization.R ├── HSVencoding.R ├── Image_resolution_switch.R ├── Mask_functions.R ├── QC.R ├── RegionNeighbours.R ├── Rigid_transformation.R ├── RunNMF.R ├── Spatial_genes.R ├── Staffli.R ├── Visualization.R ├── Visualization_utilities.R ├── crop_utilities.R ├── facet_grid_SC.R ├── generics.R ├── image_processing.R ├── image_processing_utilities.R ├── manual_annotation.R ├── pre_processing.R ├── process_from_table.R └── utilities.R ├── README.md ├── STutility.Rproj ├── inst ├── CITATION └── extdata │ ├── counts │ ├── BC1.csv │ ├── BC2.csv │ ├── BC3.csv │ ├── BC4.csv │ ├── Hippo1.jpg │ ├── Hippo1.tsv.gz │ ├── Hippo2.jpg │ ├── Hippo2.tsv.gz │ ├── Hippo3.jpg │ ├── Hippo3.tsv.gz │ ├── Hippo4.jpg │ ├── Hippo4.tsv.gz │ ├── Hippo5.jpg │ ├── Hippo5.tsv.gz │ ├── Hippo6.jpg │ ├── Hippo6.tsv.gz │ ├── Hippo7.jpg │ ├── Hippo7.tsv.gz │ ├── Hippo8.jpg │ ├── Hippo8.tsv.gz │ ├── MOB1.jpg │ ├── MOB1.tsv │ ├── MOB2.jpg │ ├── MOB2.tsv │ ├── MOB3.jpg │ ├── MOB3.tsv │ ├── MOB4.jpg │ ├── MOB4.tsv │ ├── alignment_table_Hippo1.tsv.gz │ ├── alignment_table_Hippo2.tsv.gz │ ├── alignment_table_Hippo3.tsv.gz │ ├── alignment_table_Hippo4.tsv.gz │ ├── alignment_table_Hippo5.tsv.gz │ ├── alignment_table_Hippo6.tsv.gz │ ├── alignment_table_Hippo7.tsv.gz │ ├── alignment_table_Hippo8.tsv.gz │ ├── alignment_table_MOB1.tsv │ ├── alignment_table_MOB2.tsv │ ├── alignment_table_MOB3.tsv │ └── alignment_table_MOB4.tsv │ ├── metaData.csv │ ├── metaData_mmBrain.csv │ └── mouse_genes.tsv.gz └── man ├── AlignImages.Rd ├── ColorBlender.Rd ├── ConvertGeneNames.Rd ├── CorSpatialDims.Rd ├── CorSpatialGenes.Rd ├── Create3DStack.Rd ├── CreateStaffliObject.Rd ├── Create_annotation.Rd ├── CropImages.Rd ├── CustomFacetWrap.Rd ├── DimOverlay.Rd ├── DimPlot3D.Rd ├── EdgeMask.Rd ├── FactorGeneLoadingPlot.Rd ├── FeatureOverlay.Rd ├── FeaturePlot3D.Rd ├── FilterObjects.Rd ├── GetCoords.Rd ├── GetCropWindows.Rd ├── GetSpatNet.Rd ├── GetStaffli.Rd ├── HSVOverlay.Rd ├── HSVPlot.Rd ├── HSVPlot3D.Rd ├── ImagePlot.Rd ├── InputFromTable.Rd ├── LoadImages.Rd ├── ManualAlignImages.Rd ├── ManualAnnotation.Rd ├── MaskImages.Rd ├── MergeSTData.Rd ├── Merger.Rd ├── RegionNeighbours.Rd ├── RunNMF.Rd ├── ST.DimPlot.Rd ├── ST.FeaturePlot.Rd ├── ST.ImagePlot.Rd ├── ST.rgbDimPlot.Rd ├── STPlot.Rd ├── STutility-package.Rd ├── SetQuantile.Rd ├── SmoothPlot.Rd ├── Staffli-class.Rd ├── Staffli-get-methods.Rd ├── Staffli-set-methods.Rd ├── SubsetSTData.Rd ├── SummarizeAssocFeatures.Rd ├── SwitchResolution.Rd ├── Warp.Rd ├── WarpImages.Rd ├── add.margins.Rd ├── apply.transform.Rd ├── combine.tr.Rd ├── create.array.from.feature.vals.Rd ├── create.cols.from.array.Rd ├── cscale.Rd ├── dark_theme.Rd ├── draw_scalebar.Rd ├── facet_wrap_custom.Rd ├── feature.scaler.Rd ├── find.optimal.transform.Rd ├── g_legend.Rd ├── generate.map.affine.Rd ├── generate.map.rot.Rd ├── get.edges.Rd ├── get.edges.Seurat.Rd ├── get.edges.Staffli.Rd ├── getExtension.Rd ├── grid.from.staffli.Rd ├── ica_init.Rd ├── icpmat.Rd ├── iminfo.Rd ├── interpolate_2D_data.Rd ├── labelRGB.Rd ├── make.plot.Rd ├── mirror.Rd ├── names.Rd ├── obtain.array.coords.Rd ├── palette.select.Rd ├── parse.spot.file.Rd ├── plot.Rd ├── prep.sb.Rd ├── qc.scatter.Rd ├── qcGenes.Rd ├── qcSamples.Rd ├── qcSpots.Rd ├── rasterize_scatter.Rd ├── rasterlists.Rd ├── rigid.refl.Rd ├── rigid.rot.Rd ├── rigid.stretch.Rd ├── rigid.transf.Rd ├── rigid.transl.Rd ├── rnmf.Rd ├── rotate.Rd ├── samplenames.Rd ├── scale_override.Rd ├── scaled.imdims.Rd ├── scatter_HE.Rd ├── show.Rd ├── sleepy.Rd ├── slic.Rd ├── spatial_dim_plot.Rd ├── spatial_feature_plot.Rd ├── spatial_hsv_plot.Rd ├── st.load.matrix.Rd ├── stretch.Rd └── translate.Rd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbergenstrahle/STUtility/HEAD/.Rbuildignore 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