├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── new-feature-request-enhancement.md └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── Color_Palettes.R ├── Data.R ├── Deprecated.R ├── Generics.R ├── Internal_Utilities.R ├── LIGER_Internal_Utilities.R ├── LIGER_Plotting.R ├── LIGER_Utilities.R ├── Object_Conversion.R ├── Object_Utilities.R ├── Plotting_Nebulosa.R ├── Plotting_QC_Seq_10X.R ├── Plotting_QC_Seurat.R ├── Plotting_Seurat.R ├── Plotting_Seurat_Iterative.R ├── Plotting_Shared.R ├── Plotting_Statistics.R ├── Plotting_Ultilities_Themes.R ├── Plotting_Utilities_Internal.R ├── QC_Utilities_Seurat.R ├── Read_Write_Data.R ├── Reexports.R ├── Statistics.R ├── Utilities.R ├── sysdata.rda └── zzz.R ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── data-raw ├── Create_Ensembl_ID_MALAT1_Gene_Lists_scCustomize.R ├── Create_Ensembl_ID_Mito_Ribo_Hemo_Lists_scCuztomize.R ├── Create_Ensembl_IEG_Gene_Lists_scCustomize.R ├── Create_exAM_Gene_Lists_scCustomize.R ├── Create_lncRNA_Gene_Lists_scCustomize.R └── Create_msigdb_Gene_Lists_scCustomize.R ├── data ├── ensembl_exAM_list.rda ├── ensembl_hemo_id.rda ├── ensembl_ieg_list.rda ├── ensembl_lncRNA_id.rda ├── ensembl_malat1_list.rda ├── ensembl_mito_id.rda ├── ensembl_ribo_id.rda ├── exAM_gene_list.rda ├── ieg_gene_list.rda ├── lncRNA_gene_list.rda ├── msigdb_qc_ensembl_list.rda └── msigdb_qc_gene_list.rda ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── Cell_Bender_Functions.html │ ├── Cell_Bender_Functions_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ └── unnamed-chunk-22-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Color_Palettes.html │ ├── Color_Palettes_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-10-2.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-11-2.png │ │ │ ├── unnamed-chunk-11-3.png │ │ │ ├── unnamed-chunk-11-4.png │ │ │ ├── unnamed-chunk-11-5.png │ │ │ ├── unnamed-chunk-11-6.png │ │ │ ├── unnamed-chunk-11-7.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-12-2.png │ │ │ ├── unnamed-chunk-12-3.png │ │ │ ├── unnamed-chunk-12-4.png │ │ │ ├── unnamed-chunk-12-5.png │ │ │ ├── unnamed-chunk-12-6.png │ │ │ ├── unnamed-chunk-12-7.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-13-2.png │ │ │ ├── unnamed-chunk-13-3.png │ │ │ ├── unnamed-chunk-13-4.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-14-2.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-15-2.png │ │ │ ├── unnamed-chunk-15-3.png │ │ │ ├── unnamed-chunk-15-4.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-16-2.png │ │ │ ├── unnamed-chunk-16-3.png │ │ │ ├── unnamed-chunk-16-4.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-5-2.png │ │ │ ├── unnamed-chunk-5-3.png │ │ │ ├── unnamed-chunk-5-4.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-6-2.png │ │ │ ├── unnamed-chunk-6-3.png │ │ │ ├── unnamed-chunk-6-4.png │ │ │ ├── unnamed-chunk-6-5.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-7-2.png │ │ │ ├── unnamed-chunk-7-3.png │ │ │ ├── unnamed-chunk-7-4.png │ │ │ ├── unnamed-chunk-7-5.png │ │ │ ├── unnamed-chunk-7-6.png │ │ │ ├── unnamed-chunk-7-7.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-8-2.png │ │ │ ├── unnamed-chunk-8-3.png │ │ │ ├── unnamed-chunk-8-4.png │ │ │ └── unnamed-chunk-9-1.png │ ├── FAQ.html │ ├── Gene_Expression_Plotting.html │ ├── Gene_Expression_Plotting_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-100-1.png │ │ │ ├── unnamed-chunk-101-1.png │ │ │ ├── unnamed-chunk-102-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-32-1.png │ │ │ ├── unnamed-chunk-33-1.png │ │ │ ├── unnamed-chunk-34-1.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-36-1.png │ │ │ ├── unnamed-chunk-37-1.png │ │ │ ├── unnamed-chunk-38-1.png │ │ │ ├── unnamed-chunk-39-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-41-1.png │ │ │ ├── unnamed-chunk-42-1.png │ │ │ ├── unnamed-chunk-43-1.png │ │ │ ├── unnamed-chunk-44-1.png │ │ │ ├── unnamed-chunk-45-1.png │ │ │ ├── unnamed-chunk-46-1.png │ │ │ ├── unnamed-chunk-47-1.png │ │ │ ├── unnamed-chunk-48-1.png │ │ │ ├── unnamed-chunk-49-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-50-1.png │ │ │ ├── unnamed-chunk-51-1.png │ │ │ ├── unnamed-chunk-52-1.png │ │ │ ├── unnamed-chunk-53-1.png │ │ │ ├── unnamed-chunk-54-1.png │ │ │ ├── unnamed-chunk-55-1.png │ │ │ ├── unnamed-chunk-56-1.png │ │ │ ├── unnamed-chunk-57-1.png │ │ │ ├── unnamed-chunk-58-1.png │ │ │ ├── unnamed-chunk-59-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-60-1.png │ │ │ ├── unnamed-chunk-61-1.png │ │ │ ├── unnamed-chunk-62-1.png │ │ │ ├── unnamed-chunk-63-1.png │ │ │ ├── unnamed-chunk-64-1.png │ │ │ ├── unnamed-chunk-65-1.png │ │ │ ├── unnamed-chunk-66-1.png │ │ │ ├── unnamed-chunk-67-1.png │ │ │ ├── unnamed-chunk-68-1.png │ │ │ ├── unnamed-chunk-69-1.png │ │ │ ├── unnamed-chunk-70-1.png │ │ │ ├── unnamed-chunk-71-1.png │ │ │ ├── unnamed-chunk-72-1.png │ │ │ ├── unnamed-chunk-73-1.png │ │ │ ├── unnamed-chunk-74-1.png │ │ │ ├── unnamed-chunk-75-1.png │ │ │ ├── unnamed-chunk-76-1.png │ │ │ ├── unnamed-chunk-77-1.png │ │ │ ├── unnamed-chunk-78-1.png │ │ │ ├── unnamed-chunk-79-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-80-1.png │ │ │ ├── unnamed-chunk-81-1.png │ │ │ ├── unnamed-chunk-82-1.png │ │ │ ├── unnamed-chunk-83-1.png │ │ │ ├── unnamed-chunk-84-1.png │ │ │ ├── unnamed-chunk-85-1.png │ │ │ ├── unnamed-chunk-86-1.png │ │ │ ├── unnamed-chunk-87-1.png │ │ │ ├── unnamed-chunk-88-1.png │ │ │ ├── unnamed-chunk-89-1.png │ │ │ ├── unnamed-chunk-90-1.png │ │ │ ├── unnamed-chunk-91-1.png │ │ │ ├── unnamed-chunk-92-1.png │ │ │ ├── unnamed-chunk-93-1.png │ │ │ ├── unnamed-chunk-94-1.png │ │ │ ├── unnamed-chunk-95-1.png │ │ │ ├── unnamed-chunk-96-1.png │ │ │ ├── unnamed-chunk-97-1.png │ │ │ ├── unnamed-chunk-98-1.png │ │ │ └── unnamed-chunk-99-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Helpers_and_Utilities.html │ ├── Helpers_and_Utilities_files │ │ ├── figure-html │ │ │ └── unnamed-chunk-29-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Installation.html │ ├── Iterative_Plotting.html │ ├── LIGER_Functions.html │ ├── LIGER_Functions_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── Markers_and_Cluster_Annotation.html │ ├── Markers_and_Cluster_Annotation_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Misc_Functions.html │ ├── Object_Conversion.html │ ├── Object_Conversion_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Object_QC_Functions.html │ ├── Object_QC_Functions_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-23-2.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ └── unnamed-chunk-30-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── QC_Plots.html │ ├── QC_Plots_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Read_and_Write_Functions.html │ ├── Sequencing_QC_Plots.html │ ├── Sequencing_QC_Plots_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Spatial_Plotting.html │ ├── Spatial_Plotting_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-4-1.png │ ├── Statistics.html │ ├── Statistics_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Update_Gene_Symbols.html │ ├── Update_Gene_Symbols_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── articles │ │ ├── Cell_Bender_Functions.html │ │ ├── Color_Palettes.html │ │ ├── FAQ.html │ │ ├── Gene_Expression_Plotting.html │ │ ├── Helpers_and_Utilities.html │ │ ├── Installation.html │ │ ├── Iterative_Plotting.html │ │ ├── LIGER_Functions.html │ │ ├── Markers_and_Cluster_Annotation.html │ │ ├── Misc_Functions.html │ │ ├── Object_Conversion.html │ │ ├── Object_QC_Functions.html │ │ ├── QC_Plots.html │ │ ├── Read_and_Write_Functions.html │ │ ├── Sequencing_QC_Plots.html │ │ ├── Spatial_Plotting.html │ │ ├── Statistics.html │ │ ├── Update_Gene_Symbols.html │ │ └── cNMF_Functionality.html │ ├── cNMF_Functionality.html │ ├── cNMF_Functionality_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Add_Alt_Feature_ID.html │ ├── Add_CellBender_Diff.html │ ├── Add_Cell_Complexity.Seurat.html │ ├── Add_Cell_Complexity.html │ ├── Add_Cell_Complexity.liger.html │ ├── Add_Cell_Complexity_LIGER.html │ ├── Add_Cell_Complexity_Seurat.html │ ├── Add_Cell_QC_Metrics.Seurat.html │ ├── Add_Cell_QC_Metrics.html │ ├── Add_Cell_QC_Metrics.liger.html │ ├── Add_Hemo.Seurat.html │ ├── Add_Hemo.html │ ├── Add_Hemo.liger.html │ ├── Add_MALAT1_Threshold.Seurat.html │ ├── Add_MALAT1_Threshold.html │ ├── Add_Mito_Ribo.Seurat.html │ ├── Add_Mito_Ribo.html │ ├── Add_Mito_Ribo.liger.html │ ├── Add_Mito_Ribo_LIGER.html │ ├── Add_Mito_Ribo_Seurat.html │ ├── Add_Pct_Diff.html │ ├── Add_Sample_Meta.html │ ├── Add_Top_Gene_Pct.Seurat.html │ ├── Add_Top_Gene_Pct.html │ ├── Add_Top_Gene_Pct.liger.html │ ├── Add_Top_Gene_Pct_Seurat.html │ ├── Barcode_Plot.html │ ├── Blank_Theme-1.png │ ├── Blank_Theme.html │ ├── Case_Check.html │ ├── CellBender_Diff_Plot.html │ ├── CellBender_Feature_Diff.html │ ├── Cell_Highlight_Plot-1.png │ ├── Cell_Highlight_Plot.html │ ├── Cells.html │ ├── Cells_by_Identities_LIGER.html │ ├── Cells_per_Sample.html │ ├── Change_Delim_All.html │ ├── Change_Delim_Prefix.html │ ├── Change_Delim_Suffix.html │ ├── CheckMatrix_scCustom.html │ ├── Cluster_Highlight_Plot-1.png │ ├── Cluster_Highlight_Plot.html │ ├── Cluster_Stats_All_Samples.html │ ├── Clustered_DotPlot-1.png │ ├── Clustered_DotPlot-2.png │ ├── Clustered_DotPlot-3.png │ ├── Clustered_DotPlot.html │ ├── ColorBlind_Pal-1.png │ ├── ColorBlind_Pal.html │ ├── Convert_Assay.html │ ├── Copy_From_GCP.html │ ├── Copy_To_GCP.html │ ├── Create_10X_H5.html │ ├── Create_CellBender_Merged_Seurat.html │ ├── Create_Cluster_Annotation_File.html │ ├── Dark2_Pal-1.png │ ├── Dark2_Pal.html │ ├── Dataset_Size_LIGER.html │ ├── DimPlot_All_Samples-1.png │ ├── DimPlot_All_Samples.html │ ├── DimPlot_LIGER.html │ ├── DimPlot_scCustom-1.png │ ├── DimPlot_scCustom.html │ ├── DiscretePalette_scCustomize-1.png │ ├── DiscretePalette_scCustomize.html │ ├── DotPlot_scCustom-1.png │ ├── DotPlot_scCustom.html │ ├── ElbowPlot_scCustom-1.png │ ├── ElbowPlot_scCustom.html │ ├── Embeddings.html │ ├── Extract_Modality.html │ ├── Extract_Sample_Meta.html │ ├── Extract_Top_Markers.html │ ├── Factor_Cor_Plot.html │ ├── FeaturePlot_DualAssay.html │ ├── FeaturePlot_scCustom-1.png │ ├── FeaturePlot_scCustom.html │ ├── FeatureScatter_scCustom-1.png │ ├── FeatureScatter_scCustom.html │ ├── Feature_Present.html │ ├── Features.html │ ├── Fetch_Meta.Seurat.html │ ├── Fetch_Meta.html │ ├── Fetch_Meta.liger.html │ ├── Find_Factor_Cor.html │ ├── Gene_Present.html │ ├── Get_Reference_LIGER.html │ ├── Hue_Pal-1.png │ ├── Hue_Pal.html │ ├── Idents.html │ ├── Iterate_Barcode_Rank_Plot.html │ ├── Iterate_Cluster_Highlight_Plot.html │ ├── Iterate_DimPlot_bySample.html │ ├── Iterate_FeaturePlot_scCustom.html │ ├── Iterate_Meta_Highlight_Plot.html │ ├── Iterate_PC_Loading_Plots.html │ ├── Iterate_Plot_Density_Custom.html │ ├── Iterate_Plot_Density_Joint.html │ ├── Iterate_VlnPlot_scCustom.html │ ├── JCO_Four-1.png │ ├── JCO_Four.html │ ├── LIGER_Features.html │ ├── Liger_to_Seurat.html │ ├── MAD_Stats.html │ ├── Map_New_Meta.html │ ├── Median_Stats.html │ ├── Merge_Seurat_List.html │ ├── Merge_Sparse_Data_All.html │ ├── Merge_Sparse_Multimodal_All.html │ ├── Meta_Highlight_Plot-1.png │ ├── Meta_Highlight_Plot.html │ ├── Meta_Numeric.html │ ├── Meta_Present.html │ ├── Meta_Present_LIGER.html │ ├── Meta_Remove_Seurat.html │ ├── Move_Legend-1.png │ ├── Move_Legend.html │ ├── NavyAndOrange-1.png │ ├── NavyAndOrange.html │ ├── PC_Plotting-1.png │ ├── PC_Plotting.html │ ├── PalettePlot-1.png │ ├── PalettePlot.html │ ├── Percent_Expressing.html │ ├── Plot_Cells_per_Sample.html │ ├── Plot_Density_Custom-1.png │ ├── Plot_Density_Custom.html │ ├── Plot_Density_Joint_Only-1.png │ ├── Plot_Density_Joint_Only.html │ ├── Plot_Median_Genes-1.png │ ├── Plot_Median_Genes.html │ ├── Plot_Median_Mito.html │ ├── Plot_Median_Other.html │ ├── Plot_Median_UMIs-1.png │ ├── Plot_Median_UMIs.html │ ├── Proportion_Plot-1.png │ ├── Proportion_Plot.html │ ├── Proportion_Plot_per_Sample.html │ ├── Pull_Cluster_Annotation.html │ ├── Pull_Directory_List.html │ ├── QC_Histogram.html │ ├── QC_Plot_GenevsFeature.html │ ├── QC_Plot_UMIvsFeature.html │ ├── QC_Plot_UMIvsGene-1.png │ ├── QC_Plot_UMIvsGene.html │ ├── QC_Plots_Combined_Vln.html │ ├── QC_Plots_Complexity-1.png │ ├── QC_Plots_Complexity.html │ ├── QC_Plots_Feature.html │ ├── QC_Plots_Genes-1.png │ ├── QC_Plots_Genes.html │ ├── QC_Plots_Mito.html │ ├── QC_Plots_UMIs-1.png │ ├── QC_Plots_UMIs.html │ ├── Random_Cells_Downsample.html │ ├── ReFilter_SeuratObject.html │ ├── Read10X_GEO.html │ ├── Read10X_Multi_Directory.html │ ├── Read10X_h5_GEO.html │ ├── Read10X_h5_Multi_Directory.html │ ├── Read_Add_cNMF.html │ ├── Read_CellBender_h5_Mat.html │ ├── Read_CellBender_h5_Multi_Directory.html │ ├── Read_CellBender_h5_Multi_File.html │ ├── Read_GEO_Delim.html │ ├── Read_Metrics_10X.html │ ├── Read_Metrics_CellBender.html │ ├── Reduction_Loading_Present.html │ ├── Rename_Clusters.Seurat.html │ ├── Rename_Clusters.html │ ├── Rename_Clusters.liger.html │ ├── Replace_Suffix.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Seq_QC_Plot_Alignment_Combined.html │ ├── Seq_QC_Plot_Antisense.html │ ├── Seq_QC_Plot_Basic_Combined.html │ ├── Seq_QC_Plot_Exonic.html │ ├── Seq_QC_Plot_Genes.html │ ├── Seq_QC_Plot_Genome.html │ ├── Seq_QC_Plot_Intergenic.html │ ├── Seq_QC_Plot_Intronic.html │ ├── Seq_QC_Plot_Number_Cells.html │ ├── Seq_QC_Plot_Reads_in_Cells.html │ ├── Seq_QC_Plot_Reads_per_Cell.html │ ├── Seq_QC_Plot_Saturation.html │ ├── Seq_QC_Plot_Total_Genes.html │ ├── Seq_QC_Plot_Transcriptome.html │ ├── Seq_QC_Plot_UMIs.html │ ├── Setup_scRNAseq_Project.html │ ├── Single_Color_Palette-1.png │ ├── Single_Color_Palette.html │ ├── SpatialDimPlot_scCustom.html │ ├── Split_FeatureScatter-1.png │ ├── Split_FeatureScatter.html │ ├── Split_Layers.html │ ├── Split_Vector.html │ ├── Stacked_VlnPlot-1.png │ ├── Stacked_VlnPlot.html │ ├── Store_Misc_Info_Seurat.html │ ├── Store_Palette_Seurat.html │ ├── Subset_LIGER.html │ ├── Top_Genes_Factor.html │ ├── UnRotate_X-1.png │ ├── UnRotate_X.html │ ├── Updated_HGNC_Symbols.html │ ├── Updated_MGI_Symbols.html │ ├── VariableFeaturePlot_scCustom-1.png │ ├── VariableFeaturePlot_scCustom.html │ ├── Variable_Features_ALL_LIGER.html │ ├── VlnPlot_scCustom-1.png │ ├── VlnPlot_scCustom.html │ ├── WhichCells.html │ ├── as.LIGER.Seurat.html │ ├── as.LIGER.html │ ├── as.LIGER.list.html │ ├── as.Seurat.html │ ├── as.anndata.Seurat.html │ ├── as.anndata.html │ ├── as.anndata.liger.html │ ├── deprecated.html │ ├── ensembl_exAM_list.html │ ├── ensembl_hemo_id.html │ ├── ensembl_ieg_list.html │ ├── ensembl_lncRNA_id.html │ ├── ensembl_malat1_list.html │ ├── ensembl_mito_id.html │ ├── ensembl_ribo_id.html │ ├── exAM_Scoring.html │ ├── exAM_gene_list.html │ ├── figures │ │ ├── assets │ │ │ ├── Barcode_Rank_Plot_Example.jpg │ │ │ ├── Iterate_named_plots.png │ │ │ ├── Read10X_GEO.png │ │ │ ├── annotation_info.png │ │ │ ├── delim_default.png │ │ │ ├── geo_merged.png │ │ │ ├── malat1_example.png │ │ │ ├── multimodal.png │ │ │ └── renamed.png │ │ ├── lifecycle-archived.svg │ │ ├── lifecycle-defunct.svg │ │ ├── lifecycle-deprecated.svg │ │ ├── lifecycle-experimental.svg │ │ ├── lifecycle-maturing.svg │ │ ├── lifecycle-questioning.svg │ │ ├── lifecycle-stable.svg │ │ ├── lifecycle-superseded.svg │ │ └── scCustomize_Logo.svg │ ├── ieg_gene_list.html │ ├── index.html │ ├── lncRNA_gene_list.html │ ├── msigdb_qc_ensembl_list.html │ ├── msigdb_qc_gene_list.html │ ├── plotFactors_scCustom.html │ ├── reexports.html │ ├── scCustomize-package.html │ ├── scCustomize.html │ ├── scCustomize_Palette-1.png │ ├── scCustomize_Palette.html │ ├── seq_zeros.html │ ├── theme_ggprism_mod-1.png │ ├── theme_ggprism_mod.html │ ├── viridis_dark_high.html │ ├── viridis_inferno_dark_high.html │ ├── viridis_inferno_light_high.html │ ├── viridis_light_high.html │ ├── viridis_magma_dark_high.html │ ├── viridis_magma_light_high.html │ ├── viridis_plasma_light_high.html │ └── viridis_shortcut.html └── sitemap.xml ├── index.md ├── inst └── pkgdown.yml ├── man ├── Add_Alt_Feature_ID.Rd ├── Add_CellBender_Diff.Rd ├── Add_Cell_Complexity.Rd ├── Add_Cell_QC_Metrics.Rd ├── Add_Hemo.Rd ├── Add_MALAT1_Threshold.Rd ├── Add_Mito_Ribo.Rd ├── Add_Pct_Diff.Rd ├── Add_Sample_Meta.Rd ├── Add_Top_Gene_Pct.Rd ├── Barcode_Plot.Rd ├── Blank_Theme.Rd ├── Case_Check.Rd ├── CellBender_Diff_Plot.Rd ├── CellBender_Feature_Diff.Rd ├── Cell_Highlight_Plot.Rd ├── Cells.Rd ├── Cells_by_Identities_LIGER.Rd ├── Cells_per_Sample.Rd ├── Change_Delim_All.Rd ├── Change_Delim_Prefix.Rd ├── Change_Delim_Suffix.Rd ├── CheckMatrix_scCustom.Rd ├── Cluster_Highlight_Plot.Rd ├── Cluster_Stats_All_Samples.Rd ├── Clustered_DotPlot.Rd ├── ColorBlind_Pal.Rd ├── Convert_Assay.Rd ├── Copy_From_GCP.Rd ├── Copy_To_GCP.Rd ├── Create_10X_H5.Rd ├── Create_CellBender_Merged_Seurat.Rd ├── Create_Cluster_Annotation_File.Rd ├── Dark2_Pal.Rd ├── Dataset_Size_LIGER.Rd ├── DimPlot_All_Samples.Rd ├── DimPlot_LIGER.Rd ├── DimPlot_scCustom.Rd ├── DiscretePalette_scCustomize.Rd ├── DotPlot_scCustom.Rd ├── ElbowPlot_scCustom.Rd ├── Embeddings.Rd ├── Extract_Modality.Rd ├── Extract_Sample_Meta.Rd ├── Extract_Top_Markers.Rd ├── Factor_Cor_Plot.Rd ├── FeaturePlot_DualAssay.Rd ├── FeaturePlot_scCustom.Rd ├── FeatureScatter_scCustom.Rd ├── Feature_Present.Rd ├── Features.Rd ├── Fetch_Meta.Rd ├── Find_Factor_Cor.Rd ├── Get_Reference_LIGER.Rd ├── Hue_Pal.Rd ├── Idents.Rd ├── Iterate_Barcode_Rank_Plot.Rd ├── Iterate_Cluster_Highlight_Plot.Rd ├── Iterate_DimPlot_bySample.Rd ├── Iterate_FeaturePlot_scCustom.Rd ├── Iterate_Meta_Highlight_Plot.Rd ├── Iterate_PC_Loading_Plots.Rd ├── Iterate_Plot_Density_Custom.Rd ├── Iterate_Plot_Density_Joint.Rd ├── Iterate_VlnPlot_scCustom.Rd ├── JCO_Four.Rd ├── MAD_Stats.Rd ├── Map_New_Meta.Rd ├── Median_Stats.Rd ├── Merge_Seurat_List.Rd ├── Merge_Sparse_Data_All.Rd ├── Merge_Sparse_Multimodal_All.Rd ├── Meta_Highlight_Plot.Rd ├── Meta_Numeric.Rd ├── Meta_Present.Rd ├── Meta_Remove_Seurat.Rd ├── Move_Legend.Rd ├── NavyAndOrange.Rd ├── PC_Plotting.Rd ├── PalettePlot.Rd ├── Percent_Expressing.Rd ├── Plot_Cells_per_Sample.Rd ├── Plot_Density_Custom.Rd ├── Plot_Density_Joint_Only.Rd ├── Plot_Median_Genes.Rd ├── Plot_Median_Mito.Rd ├── Plot_Median_Other.Rd ├── Plot_Median_UMIs.Rd ├── Proportion_Plot.Rd ├── Proportion_Plot_per_Sample.Rd ├── Pull_Cluster_Annotation.Rd ├── Pull_Directory_List.Rd ├── QC_Histogram.Rd ├── QC_Plot_GenevsFeature.Rd ├── QC_Plot_UMIvsFeature.Rd ├── QC_Plot_UMIvsGene.Rd ├── QC_Plots_Combined_Vln.Rd ├── QC_Plots_Complexity.Rd ├── QC_Plots_Feature.Rd ├── QC_Plots_Genes.Rd ├── QC_Plots_Mito.Rd ├── QC_Plots_UMIs.Rd ├── Random_Cells_Downsample.Rd ├── ReFilter_SeuratObject.Rd ├── Read10X_GEO.Rd ├── Read10X_Multi_Directory.Rd ├── Read10X_h5_GEO.Rd ├── Read10X_h5_Multi_Directory.Rd ├── Read_Add_cNMF.Rd ├── Read_CellBender_h5_Mat.Rd ├── Read_CellBender_h5_Multi_Directory.Rd ├── Read_CellBender_h5_Multi_File.Rd ├── Read_GEO_Delim.Rd ├── Read_Metrics_10X.Rd ├── Read_Metrics_CellBender.Rd ├── Reduction_Loading_Present.Rd ├── Rename_Clusters.Rd ├── Replace_Suffix.Rd ├── Seq_QC_Plot_Alignment_Combined.Rd ├── Seq_QC_Plot_Antisense.Rd ├── Seq_QC_Plot_Basic_Combined.Rd ├── Seq_QC_Plot_Exonic.Rd ├── Seq_QC_Plot_Genes.Rd ├── Seq_QC_Plot_Genome.Rd ├── Seq_QC_Plot_Intergenic.Rd ├── Seq_QC_Plot_Intronic.Rd ├── Seq_QC_Plot_Number_Cells.Rd ├── Seq_QC_Plot_Reads_in_Cells.Rd ├── Seq_QC_Plot_Reads_per_Cell.Rd ├── Seq_QC_Plot_Saturation.Rd ├── Seq_QC_Plot_Total_Genes.Rd ├── Seq_QC_Plot_Transcriptome.Rd ├── Seq_QC_Plot_UMIs.Rd ├── Setup_scRNAseq_Project.Rd ├── Single_Color_Palette.Rd ├── SpatialDimPlot_scCustom.Rd ├── Split_Layers.Rd ├── Split_Vector.Rd ├── Stacked_VlnPlot.Rd ├── Store_Misc_Info_Seurat.Rd ├── Store_Palette_Seurat.Rd ├── Subset_LIGER.Rd ├── Top_Genes_Factor.Rd ├── UnRotate_X.Rd ├── Updated_HGNC_Symbols.Rd ├── Updated_MGI_Symbols.Rd ├── VariableFeaturePlot_scCustom.Rd ├── Variable_Features_ALL_LIGER.Rd ├── VlnPlot_scCustom.Rd ├── WhichCells.Rd ├── as.LIGER.Rd ├── as.Seurat.Rd ├── as.anndata.Rd ├── ensembl_exAM_list.Rd ├── ensembl_hemo_id.Rd ├── ensembl_ieg_list.Rd ├── ensembl_lncRNA_id.Rd ├── ensembl_malat1_list.Rd ├── ensembl_mito_id.Rd ├── ensembl_ribo_id.Rd ├── exAM_Scoring.Rd ├── exAM_gene_list.Rd ├── figures │ ├── assets │ │ ├── Iterate_named_plots.png │ │ ├── Read10X_GEO.png │ │ ├── annotation_info.png │ │ ├── delim_default.png │ │ ├── geo_merged.png │ │ ├── multimodal.png │ │ └── renamed.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── scCustomize_Logo.svg ├── ieg_gene_list.Rd ├── lncRNA_gene_list.Rd ├── msigdb_qc_ensembl_list.Rd ├── msigdb_qc_gene_list.Rd ├── plotFactors_scCustom.Rd ├── reexports.Rd ├── scCustomize-package.Rd ├── scCustomize_Palette.Rd ├── seq_zeros.Rd ├── theme_ggprism_mod.Rd └── viridis_shortcut.Rd ├── scCustomize.Rproj └── vignettes 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