Man pages for samuel-marsh/scCustomize
Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
| Add_Alt_Feature_ID | Add Alternative Feature IDs |
| Add_CellBender_Diff | Calculate and add differences post-cell bender analysis |
| Add_Cell_Complexity | Add Cell Complexity |
| Add_Cell_QC_Metrics | Add Multiple Cell Quality Control Values with Single Function |
| Add_Hemo | Add Hemoglobin percentages |
| Add_Mito_Ribo | Add Mito and Ribo percentages |
| Add_Pct_Diff | Add percentage difference to DE results |
| Add_Sample_Meta | Add Sample Level Meta Data |
| Add_Top_Gene_Pct | Add Percent of High Abundance Genes |
| as.anndata | Convert objects to anndata objects |
| as.LIGER | Convert objects to LIGER objects |
| as.Seurat | Convert objects to 'Seurat' objects |
| Barcode_Plot | Create Barcode Rank Plot |
| Blank_Theme | Blank Theme |
| Case_Check | Check for alternate case features |
| CellBender_Diff_Plot | Plot Number of Cells/Nuclei per Sample |
| CellBender_Feature_Diff | CellBender Feature Differences |
| Cell_Highlight_Plot | Meta Highlight Plot |
| Cells | Extract Cells from LIGER Object |
| Cells_by_Identities_LIGER | Extract Cells by identity |
| Cells_per_Sample | Cells per Sample |
| 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 |
| Convert_Assay | Convert between Seurat Assay types |
| 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 |
| Dark2_Pal | Dark2 Palette |
| deprecated | Deprecated functions *[Deprecated]* |
| 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 |
| Embeddings | Extract matrix of embeddings |
| ensembl_hemo_id | Ensembl Hemo IDs |
| ensembl_ieg_list | Immediate Early Gene (IEG) gene lists |
| ensembl_mito_id | Ensembl Mito IDs |
| ensembl_ribo_id | Ensembl Ribo IDs |
| Extract_Modality | Extract multi-modal data into list by modality |
| Extract_Sample_Meta | Extract sample level meta.data |
| Extract_Top_Markers | Extract Top N Marker Genes |
| Factor_Cor_Plot | Factor Correlation Plot |
| FeaturePlot_DualAssay | Customize FeaturePlot of two assays |
| FeaturePlot_scCustom | Customize FeaturePlot |
| Feature_Present | Check if genes/features are present |
| Features | Extract Features from LIGER Object |
| FeatureScatter_scCustom | Modified version of FeatureScatter |
| Fetch_Meta | Get meta data from object |
| Find_Factor_Cor | Find Factor Correlations |
| Hue_Pal | Hue_Pal |
| Idents | Extract or set default identities from object |
| ieg_gene_list | Immediate Early Gene (IEG) gene lists |
| Iterate_Barcode_Rank_Plot | Iterative Barcode Rank Plots |
| 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... |
| Iterate_VlnPlot_scCustom | Iterative Plotting of Gene Lists using VlnPlot_scCustom |
| JCO_Four | Four Color Palette (JCO) |
| Liger_to_Seurat | Create a Seurat object containing the data from a liger... |
| MAD_Stats | Median Absolute Deviation Statistics |
| Median_Stats | Median Statistics |
| Merge_Seurat_List | Merge a list of Seurat Objects |
| Merge_Sparse_Data_All | Merge a list of Sparse Matrices |
| Merge_Sparse_Multimodal_All | Merge a list of Sparse Matrices contain multi-modal data. |
| Meta_Highlight_Plot | Meta Highlight Plot |
| Meta_Numeric | Check if meta data columns are numeric |
| Meta_Present | Check if meta data are present |
| Meta_Remove_Seurat | Remove meta data columns containing Seurat Defaults |
| Move_Legend | Move Legend Position |
| msigdb_qc_ensembl_list | QC Gene Lists |
| msigdb_qc_gene_list | QC Gene Lists |
| NavyAndOrange | Navy and Orange Dual Color Palette |
| PalettePlot | Plot color palette in viewer |
| PC_Plotting | PC Plots |
| Percent_Expressing | Calculate percent of expressing cells |
| 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 |
| plotFactors_scCustom | Customized version of plotFactors |
| 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 |
| Proportion_Plot | Cell Proportion Plot |
| Pull_Cluster_Annotation | Pull cluster information from annotation csv file. |
| Pull_Directory_List | Pull Directory List |
| QC_Histogram | QC Histogram Plots |
| QC_Plot_GenevsFeature | QC Plots Genes vs Misc |
| 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_UMIvsFeature | QC Plots UMI vs Misc |
| QC_Plot_UMIvsGene | QC Plots Genes vs UMIs |
| Random_Cells_Downsample | Randomly downsample by identity |
| 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... |
| 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 |
| Read_Metrics_CellBender | Read Overall Statistics from CellBender |
| Reduction_Loading_Present | Check if reduction loadings are present |
| reexports | Objects exported from other packages |
| Rename_Clusters | Rename Clusters |
| Replace_Suffix | Replace barcode suffixes |
| scCustomize-package | scCustomize: Custom Visualizations & Functions for... |
| 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 |
| seq_zeros | Create sequence with zeros |
| Setup_scRNAseq_Project | Setup project directory structure |
| Single_Color_Palette | Single Color Palettes for Plotting |
| SpatialDimPlot_scCustom | SpatialDimPlot with modified default settings |
| Split_Layers | Split Seurat object into layers |
| Split_Vector | Split vector into list |
| Stacked_VlnPlot | Stacked Violin Plot |
| Store_Misc_Info_Seurat | Store misc data in Seurat object |
| Store_Palette_Seurat | Store color palette in Seurat object |
| Subset_LIGER | Subset LIGER object |
| theme_ggprism_mod | Modified ggprism theme |
| Top_Genes_Factor | Extract top loading genes for LIGER factor |
| UnRotate_X | Unrotate x axis on VlnPlot |
| Updated_HGNC_Symbols | Update HGNC Gene Symbols |
| Updated_MGI_Symbols | Update MGI Gene Symbols |
| VariableFeaturePlot_scCustom | Custom Labeled Variable Features Plot |
| Variable_Features_ALL_LIGER | Perform variable gene selection over whole dataset |
| viridis_shortcut | Viridis Shortcuts |
| VlnPlot_scCustom | VlnPlot with modified default settings |
| WhichCells | Extract Cells for particular identity |
