Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
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Documentation for package ‘scCustomize’ version 1.1.1
Help Pages
A B C D E F G H I J L M N P Q R S T U V
-- A --
| Add_CellBender_Diff | Calculate and add differences post-cell bender analysis |
| Add_Cell_Complexity_LIGER | Add Cell Complexity Value |
| Add_Cell_Complexity_Seurat | Add Cell Complexity Value |
| Add_Mito_Ribo_LIGER | Add Mito and Ribo percentages to LIGER |
| Add_Mito_Ribo_Seurat | Add Mito and Ribo percentages |
| Add_Pct_Diff | Add percentage difference to DE results |
| Add_Sample_Meta | Add Sample Level Meta Data |
-- B --
| Blank_Theme | Blank Theme |
-- C --
| Case_Check | Check for alternate case features Checks Seurat object for the presence of features with the same spelling but alternate case. |
| CellBender_Diff_Plot | Plot Number of Cells/Nuclei per Sample |
| CellBender_Feature_Diff | CellBender Feature Differences |
| Cell_Highlight_Plot | Meta Highlight Plot |
| Change_Delim_All | Change all delimiters in cell name |
| Change_Delim_Prefix | Change barcode prefix delimiter |
| Change_Delim_Suffix | Change barcode suffix delimiter |
| CheckMatrix_scCustom | Check Matrix Validity |
| Clustered_DotPlot | Clustered DotPlot |
| Cluster_Highlight_Plot | Cluster Highlight Plot |
| Cluster_Stats_All_Samples | Calculate Cluster Stats |
| ColorBlind_Pal | Color Universal Design Short Palette |
| Copy_From_GCP | Copy folder from GCP bucket from R Console |
| Copy_To_GCP | Copy folder to GCP bucket from R Console |
| Create_10X_H5 | Create H5 from 10X Outputs |
| Create_CellBender_Merged_Seurat | Create Seurat Object with Cell Bender and Raw data |
| Create_Cluster_Annotation_File | Create cluster annotation csv file |
-- D --
| Dark2_Pal | Dark2 Palette |
| DimPlot_All_Samples | DimPlot by Meta Data Column |
| DimPlot_LIGER | DimPlot LIGER Version |
| DimPlot_scCustom | DimPlot with modified default settings |
| DiscretePalette_scCustomize | Discrete color palettes |
| DotPlot_scCustom | Customized DotPlot |
-- E --
| ensembl_mito_id | Ensembl Mito IDs |
| ensembl_ribo_id | Ensembl Ribo IDs |
| Extract_Sample_Meta | Extract sample level meta.data |
| Extract_Top_Markers | Extract Top N Marker Genes |
-- F --
| FeaturePlot_DualAssay | Customize FeaturePlot of two assays |
| FeaturePlot_scCustom | Customize FeaturePlot |
| Fetch_Meta | Get meta data from object |
| Fetch_Meta.liger | Get meta data from object |
| Fetch_Meta.Seurat | Get meta data from object |
-- G --
| Gene_Present | Check if genes/features are present |
-- H --
| Hue_Pal | Hue_Pal |
-- I --
| Iterate_Cluster_Highlight_Plot | Iterate Cluster Highlight Plot |
| Iterate_DimPlot_bySample | Iterate DimPlot By Sample |
| Iterate_FeaturePlot_scCustom | Iterative Plotting of Gene Lists using Custom FeaturePlots |
| Iterate_Meta_Highlight_Plot | Iterate Meta Highlight Plot |
| Iterate_PC_Loading_Plots | Iterate PC Loading Plots |
| Iterate_Plot_Density_Custom | Iterative Plotting of Gene Lists using Custom Density Plots |
| Iterate_Plot_Density_Joint | Iterative Plotting of Gene Lists using Custom Joint Density Plots |
| Iterate_VlnPlot_scCustom | Iterative Plotting of Gene Lists using VlnPlot_scCustom |
-- J --
| JCO_Four | Four Color Palette (JCO) |
-- L --
| Liger_to_Seurat | Create a Seurat object containing the data from a liger object |
-- M --
| Median_Stats | Median Statistics |
| Merge_Seurat_List | Merge a list of Seurat Objects |
| Merge_Sparse_Data_All | Merge a list of Sparse Matrices |
| Meta_Highlight_Plot | Meta Highlight Plot |
| Meta_Numeric | Check if meta data columns are numeric |
| Meta_Present | Check if meta data are present |
| Meta_Present_LIGER | Check if meta data are present |
| Meta_Remove_Seurat | Remove meta data columns containing Seurat Defaults |
| Move_Legend | Move Legend Position |
-- N --
| NavyAndOrange | Navy and Orange Dual Color Palette |
-- P --
| PalettePlot | Plot color palette in viewer |
| PC_Plotting | PC Plots |
| Percent_Expressing | Calculate percent of expressing cells |
| plotFactors_scCustom | Customized version of plotFactors |
| Plot_Cells_per_Sample | Plot Number of Cells/Nuclei per Sample |
| Plot_Density_Custom | Nebulosa Density Plot |
| Plot_Density_Joint_Only | Nebulosa Joint Density Plot |
| Plot_Median_Genes | Plot Median Genes per Cell per Sample |
| Plot_Median_Mito | Plot Median Percent Mito per Cell per Sample |
| Plot_Median_Other | Plot Median other variable per Cell per Sample |
| Plot_Median_UMIs | Plot Median UMIs per Cell per Sample |
| Pull_Cluster_Annotation | Pull cluster information from annotation csv file. |
| Pull_Directory_List | Pull Directory List |
-- Q --
| QC_Plots_Combined_Vln | QC Plots Genes, UMIs, & % Mito |
| QC_Plots_Complexity | QC Plots Cell "Complexity" |
| QC_Plots_Feature | QC Plots Feature |
| QC_Plots_Genes | QC Plots Genes |
| QC_Plots_Mito | QC Plots Mito |
| QC_Plots_UMIs | QC Plots UMIs |
| QC_Plot_GenevsFeature | QC Plots Genes vs Misc |
| QC_Plot_UMIvsFeature | QC Plots UMI vs Misc |
| QC_Plot_UMIvsGene | QC Plots Genes vs UMIs |
-- R --
| Read10X_GEO | Load in NCBI GEO data from 10X |
| Read10X_h5_GEO | Load in NCBI GEO data from 10X in HDF5 file format |
| Read10X_h5_Multi_Directory | Load 10X h5 count matrices from multiple directories |
| Read10X_Multi_Directory | Load 10X count matrices from multiple directories |
| Read_CellBender_h5_Mat | Load CellBender h5 matrices (corrected) |
| Read_CellBender_h5_Multi_Directory | Load CellBender h5 matrices (corrected) from multiple directories |
| Read_CellBender_h5_Multi_File | Load CellBender h5 matrices (corrected) from multiple files |
| Read_GEO_Delim | Load in NCBI GEO data formatted as single file per sample |
| Read_Metrics_10X | Read Overall Statistics from 10X Cell Ranger Count |
| Rename_Clusters | Rename Cluster Seurat |
| Replace_Suffix | Replace barcode suffixes |
-- S --
| scCustomize_Palette | Color Palette Selection for scCustomize |
| Seq_QC_Plot_Alignment_Combined | QC Plots Sequencing metrics (Alignment) (Layout) |
| Seq_QC_Plot_Antisense | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_Basic_Combined | QC Plots Sequencing metrics (Layout) |
| Seq_QC_Plot_Exonic | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_Genes | QC Plots Sequencing metrics |
| Seq_QC_Plot_Genome | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_Intergenic | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_Intronic | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_Number_Cells | QC Plots Sequencing metrics |
| Seq_QC_Plot_Reads_in_Cells | QC Plots Sequencing metrics |
| Seq_QC_Plot_Reads_per_Cell | QC Plots Sequencing metrics |
| Seq_QC_Plot_Saturation | QC Plots Sequencing metrics |
| Seq_QC_Plot_Total_Genes | QC Plots Sequencing metrics |
| Seq_QC_Plot_Transcriptome | QC Plots Sequencing metrics (Alignment) |
| Seq_QC_Plot_UMIs | QC Plots Sequencing metrics |
| Setup_scRNAseq_Project | Setup project directory structure |
| Single_Color_Palette | Single Color Palettes for Plotting |
| Split_FeatureScatter | Split FeatureScatter |
| Stacked_VlnPlot | Stacked Violin Plot |
| Store_Misc_Info_Seurat | Store misc data in Seurat object |
| Store_Palette_Seurat | Store color palette in Seurat object |
-- T --
| theme_ggprism_mod | Modified ggprism theme |
| Top_Genes_Factor | Extract top loading genes for LIGER factor |
-- U --
| UnRotate_X | Unrotate x axis on VlnPlot |
-- V --
| VariableFeaturePlot_scCustom | Custom Labeled Variable Features Plot |
| Variable_Features_ALL_LIGER | Perform variable gene selection over whole dataset |
| viridis_dark_high | Viridis Shortcuts |
| viridis_inferno_dark_high | Viridis Shortcuts |
| viridis_inferno_light_high | Viridis Shortcuts |
| viridis_light_high | Viridis Shortcuts |
| viridis_magma_dark_high | Viridis Shortcuts |
| viridis_magma_light_high | Viridis Shortcuts |
| viridis_plasma_dark_high | Viridis Shortcuts |
| viridis_plasma_light_high | Viridis Shortcuts |
| VlnPlot_scCustom | VlnPlot with modified default settings |