add Add_10X_CellTypes. use base R. account for multi-modal data

NAMESPACE

@@ -37,7 +37,6 @@ S3method(FindVariableFeatures,Assay)
 S3method(FindVariableFeatures,SCTAssay)
 S3method(FindVariableFeatures,Seurat)
 S3method(FindVariableFeatures,StdAssay)
-S3method(FindVariableFeatures,V3Matrix)
 S3method(FindVariableFeatures,default)
 S3method(FoldChange,Assay)
 S3method(FoldChange,DimReduc)
@@ -61,15 +60,12 @@ S3method(LeverageScore,Seurat)
 S3method(LeverageScore,StdAssay)
 S3method(LeverageScore,default)
 S3method(LogNormalize,IterableMatrix)
-S3method(LogNormalize,V3Matrix)
-S3method(LogNormalize,data.frame)
 S3method(LogNormalize,default)
 S3method(MappingScore,AnchorSet)
 S3method(MappingScore,default)
 S3method(NormalizeData,Assay)
 S3method(NormalizeData,Seurat)
 S3method(NormalizeData,StdAssay)
-S3method(NormalizeData,V3Matrix)
 S3method(NormalizeData,default)
 S3method(ProjectCellEmbeddings,Assay)
 S3method(ProjectCellEmbeddings,IterableMatrix)
@@ -124,13 +120,9 @@ S3method(RunUMAP,default)
 S3method(SCTResults,SCTAssay)
 S3method(SCTResults,SCTModel)
 S3method(SCTResults,Seurat)
-S3method(SCTransform,Assay)
 S3method(SCTransform,IterableMatrix)
-S3method(SCTransform,Seurat)
 S3method(SCTransform,StdAssay)
-S3method(SCTransform,default)
 S3method(ScaleData,Assay)
-S3method(ScaleData,IterableMatrix)
 S3method(ScaleData,Seurat)
 S3method(ScaleData,StdAssay)
 S3method(ScaleData,default)
@@ -300,11 +292,10 @@ export(LabelPoints)
 export(LeverageScore)
 export(LinkedDimPlot)
 export(LinkedFeaturePlot)
+export(Load10X)
 export(Load10X_Spatial)
-export(Load10x)
 export(LoadAkoya)
 export(LoadAnnoyIndex)
-export(LoadCurioSeeker)
 export(LoadHuBMAPCODEX)
 export(LoadNanostring)
 export(LoadSTARmap)
@@ -358,11 +349,8 @@ export(PurpleAndYellow)
 export(RPCAIntegration)
 export(Radius)
 export(Read10X)
-export(Read10X_Coordinates)
 export(Read10X_Image)
-export(Read10X_ScaleFactors)
 export(Read10X_h5)
-export(Read10X_probe_metadata)
 export(ReadAkoya)
 export(ReadMtx)
 export(ReadNanostring)
@@ -609,6 +597,9 @@ importFrom(SeuratObject,as.Graph)
 importFrom(SeuratObject,as.Neighbor)
 importFrom(SeuratObject,as.Seurat)
 importFrom(SeuratObject,as.sparse)
+importFrom(base,file.exists)
+importFrom(base,file.path)
+importFrom(base,merge)
 importFrom(cluster,clara)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)
@@ -797,7 +788,6 @@ importFrom(plotly,plot_ly)
 importFrom(plotly,raster2uri)
 importFrom(png,readPNG)
 importFrom(progressr,progressor)
-importFrom(purrr,imap)
 importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)
@@ -889,6 +879,8 @@ importFrom(stats,setNames)
 importFrom(stats,t.test)
 importFrom(stats,var)
 importFrom(stats,wilcox.test)
+importFrom(tibble,column_to_rownames)
+importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)