{ "_id": "6a103b86acfb0bcc41c9b879", "Package": "scCustomize", "Type": "Package", "Title": "Custom Visualizations & Functions for Streamlined Analyses of\nSingle Cell Sequencing", "Description": "Collection of functions created and/or curated to aid in\nthe visualization and analysis of single-cell data using 'R'.\n'scCustomize' aims to provide 1) Customized visualizations for\naid in ease of use and to create more aesthetic and functional\nvisuals. 2) Improve speed/reproducibility of common\ntasks/pieces of code in scRNA-seq analysis with a single or\ngroup of functions. 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"topics": [ "Add_Alt_Feature_ID" ] }, { "page": "Add_Cell_Complexity", "title": "Add Cell Complexity", "concept": [ "liger_object_util", "qc_util" ], "topics": [ "Add_Cell_Complexity", "Add_Cell_Complexity.liger", "Add_Cell_Complexity.Seurat" ] }, { "page": "Add_Cell_QC_Metrics", "title": "Add Multiple Cell Quality Control Values with Single Function", "concept": [ "qc_util" ], "topics": [ "Add_Cell_QC_Metrics", "Add_Cell_QC_Metrics.liger", "Add_Cell_QC_Metrics.Seurat" ] }, { "page": "Add_CellBender_Diff", "title": "Calculate and add differences post-cell bender analysis", "concept": [ "qc_util" ], "topics": [ "Add_CellBender_Diff" ] }, { "page": "Add_Hemo", "title": "Add Hemoglobin percentages", "concept": [ "qc_util" ], "topics": [ "Add_Hemo", "Add_Hemo.liger", "Add_Hemo.Seurat" ] }, { "page": "Add_MALAT1_Threshold", "title": "Add MALAT1 QC Threshold", "concept": [ "qc_util" ], "topics": [ "Add_MALAT1_Threshold", "Add_MALAT1_Threshold.Seurat" ] }, { "page": "Add_Mito_Ribo", "title": "Add Mito and Ribo percentages", "concept": [ "liger_object_util", "qc_util" ], "topics": [ "Add_Mito_Ribo", "Add_Mito_Ribo.liger", "Add_Mito_Ribo.Seurat" ] }, { "page": "Add_Pct_Diff", "title": "Add percentage difference to DE results", "concept": [ "marker_annotation_util" ], "topics": [ "Add_Pct_Diff" ] }, { "page": "Add_Sample_Meta", "title": "Add Sample Level Meta Data", "concept": [ "get_set_util" ], "topics": [ "Add_Sample_Meta" ] }, { "page": "Add_Top_Gene_Pct", "title": "Add Percent of High Abundance Genes", "concept": [ "qc_util" ], "topics": [ "Add_Top_Gene_Pct", "Add_Top_Gene_Pct.liger", "Add_Top_Gene_Pct.Seurat" ] }, { "page": "as.anndata", "title": "Convert objects to anndata objects", "concept": [ "object_conversion" ], "topics": [ "as.anndata", "as.anndata.liger", "as.anndata.Seurat" ] }, { "page": "as.LIGER", "title": "Convert objects to LIGER objects", "concept": [ "object_conversion" ], "topics": [ "as.LIGER", "as.LIGER.list", "as.LIGER.Seurat" ] }, { "page": "as.Seurat", "title": "Convert objects to 'Seurat' objects", "concept": [ "object_conversion" ], "topics": [ "as.Seurat.liger" ] }, { "page": "Barcode_Plot", "title": "Create Barcode Rank Plot", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Barcode_Plot" ] }, { "page": "Blank_Theme", "title": "Blank Theme", "concept": [ "themes" ], "topics": [ "Blank_Theme" ] }, { "page": "Case_Check", "title": "Check for alternate case features", "concept": [ "check_util" ], "topics": [ "Case_Check" ] }, { "page": "Cell_Highlight_Plot", "title": "Meta Highlight Plot", "concept": [ "seurat_plotting" ], "topics": [ "Cell_Highlight_Plot" ] }, { "page": "CellBender_Diff_Plot", "title": "Plot Number of Cells/Nuclei per Sample", "concept": [ "stats_plotting" ], "topics": [ "CellBender_Diff_Plot" ] }, { "page": "CellBender_Feature_Diff", "title": "CellBender Feature Differences", "concept": [ "stats" ], "topics": [ "CellBender_Feature_Diff" ] }, { "page": "Cells_by_Identities_LIGER", "title": "Extract Cells by identity", "concept": [ "liger_object_util" ], "topics": [ "Cells_by_Identities_LIGER" ] }, { "page": "Cells_per_Sample", "title": "Cells per Sample", "concept": [ "stats" ], "topics": [ "Cells_per_Sample" ] }, { "page": "Cells", "title": "Extract Cells from LIGER Object", "concept": [ "liger_object_util" ], "topics": [ "Cells.liger" ] }, { "page": "Change_Delim_All", "title": "Change all delimiters in cell name", "concept": [ "barcode_util" ], "topics": [ "Change_Delim_All" ] }, { "page": "Change_Delim_Prefix", "title": "Change barcode prefix delimiter", "concept": [ "barcode_util" ], "topics": [ "Change_Delim_Prefix" ] }, { "page": "Change_Delim_Suffix", "title": "Change barcode suffix delimiter", "concept": [ "barcode_util" ], "topics": [ "Change_Delim_Suffix" ] }, { "page": "CheckMatrix_scCustom", "title": "Check Matrix Validity", "concept": [ "check_util" ], "topics": [ "CheckMatrix_scCustom" ] }, { "page": "Cluster_Highlight_Plot", "title": "Cluster Highlight Plot", "concept": [ "seurat_plotting" ], "topics": [ "Cluster_Highlight_Plot" ] }, { "page": "Cluster_Stats_All_Samples", "title": "Calculate Cluster Stats", "concept": [ "stats" ], "topics": [ "Cluster_Stats_All_Samples" ] }, { "page": "Clustered_DotPlot", "title": "Clustered DotPlot", "concept": [ "seurat_plotting" ], "topics": [ "Clustered_DotPlot" ] }, { "page": "ColorBlind_Pal", "title": "Color Universal Design Short Palette", "concept": [ "palettes" ], "topics": [ "ColorBlind_Pal" ] }, { "page": "Convert_Assay", "title": "Convert between Seurat Assay types", "concept": [ "object_conversion" ], "topics": [ "Convert_Assay" ] }, { "page": "Copy_From_GCP", "title": "Copy folder from GCP bucket from R Console", "concept": [ "organization_util" ], "topics": [ "Copy_From_GCP" ] }, { "page": "Copy_To_GCP", "title": "Copy folder to GCP bucket from R Console", "concept": [ "organization_util" ], "topics": [ "Copy_To_GCP" ] }, { "page": "Create_10X_H5", "title": "Create H5 from 10X Outputs", "concept": [ "read_&_write" ], "topics": [ "Create_10X_H5" ] }, { "page": "Create_CellBender_Merged_Seurat", "title": "Create Seurat Object with Cell Bender and Raw data", "concept": [ "read_&_write" ], "topics": [ "Create_CellBender_Merged_Seurat" ] }, { "page": "Create_Cluster_Annotation_File", "title": "Create cluster annotation csv file", "concept": [ "marker_annotation_util" ], "topics": [ "Create_Cluster_Annotation_File" ] }, { "page": "Dark2_Pal", "title": "Dark2 Palette", "concept": [ "palettes" ], "topics": [ "Dark2_Pal" ] }, { "page": "Dataset_Size_LIGER", "title": "Check size of LIGER datasets", "concept": [ "liger_object_util" ], "topics": [ "Dataset_Size_LIGER" ] }, { "page": "DimPlot_All_Samples", "title": "DimPlot by Meta Data Column", "concept": [ "seurat_plotting" ], "topics": [ "DimPlot_All_Samples" ] }, { "page": "DimPlot_LIGER", "title": "DimPlot LIGER Version", "concept": [ "liger_plotting" ], "topics": [ "DimPlot_LIGER" ] }, { "page": "DimPlot_scCustom", "title": "DimPlot with modified default settings", "concept": [ "seurat_plotting" ], "topics": [ "DimPlot_scCustom" ] }, { "page": "DiscretePalette_scCustomize", "title": "Discrete color palettes", "concept": [ "palettes" ], "topics": [ "DiscretePalette_scCustomize" ] }, { "page": "DotPlot_scCustom", "title": "Customized DotPlot", "concept": [ "seurat_plotting" ], "topics": [ "DotPlot_scCustom" ] }, { "page": "ElbowPlot_scCustom", "title": "ElbowPlot with modifications", "concept": [ "seurat_plotting" ], "topics": [ "ElbowPlot_scCustom" ] }, { "page": "Embeddings", "title": "Extract matrix of embeddings", "concept": [ "liger_object_util" ], "topics": [ "Embeddings.liger" ] }, { "page": "ensembl_exAM_list", "title": "Immediate Early Gene (IEG) gene lists", "concept": [ "data" ], "topics": [ "ensembl_exAM_list" ] }, { "page": "ensembl_hemo_id", "title": "Ensembl Hemo IDs", "concept": [ "data" ], "topics": [ "ensembl_hemo_id" ] }, { "page": "ensembl_ieg_list", "title": "Immediate Early Gene (IEG) gene lists", "concept": [ "data" ], "topics": [ "ensembl_ieg_list" ] }, { "page": "ensembl_lncRNA_id", "title": "Ensembl lncRNA IDs", "concept": [ "data" ], "topics": [ "ensembl_lncRNA_id" ] }, { "page": "ensembl_malat1_list", "title": "MALAT1 gene lists", "concept": [ "data" ], "topics": [ "ensembl_malat1_list" ] }, { "page": "ensembl_mito_id", "title": "Ensembl Mito IDs", "concept": [ "data" ], "topics": [ "ensembl_mito_id" ] }, { "page": "ensembl_ribo_id", "title": "Ensembl Ribo IDs", "concept": [ "data" ], "topics": [ "ensembl_ribo_id" ] }, { "page": "exAM_gene_list", "title": "exAM gene lists", "concept": [ "data" ], "topics": [ "exAM_gene_list" ] }, { "page": "exAM_Scoring", "title": "Add exAM Gene List Module Scores", "concept": [ "qc_util" ], "topics": [ "exAM_Scoring" ] }, { "page": "Extract_Modality", "title": "Extract multi-modal data into list by modality", "concept": [ "read_merge_util" ], "topics": [ "Extract_Modality" ] }, { "page": "Extract_Sample_Meta", "title": "Extract sample level meta.data", "concept": [ "get_set_util" ], "topics": [ "Extract_Sample_Meta" ] }, { "page": "Extract_Top_Markers", "title": "Extract Top N Marker Genes", "concept": [ "marker_annotation_util" ], "topics": [ "Extract_Top_Markers" ] }, { "page": "Factor_Cor_Plot", "title": "Factor Correlation Plot", "concept": [ "liger_plotting" ], "topics": [ "Factor_Cor_Plot" ] }, { "page": "Feature_Present", "title": "Check if genes/features are present", "concept": [ "check_util" ], "topics": [ "Feature_Present" ] }, { "page": "FeaturePlot_DualAssay", "title": "Customize FeaturePlot of two assays", "concept": [ "seurat_plotting" ], "topics": [ "FeaturePlot_DualAssay" ] }, { "page": "FeaturePlot_scCustom", "title": "Customize FeaturePlot", "concept": [ "seurat_plotting" ], "topics": [ "FeaturePlot_scCustom" ] }, { "page": "Features", "title": "Extract Features from LIGER Object", "concept": [ "liger_object_util" ], "topics": [ "Features.liger" ] }, { "page": "FeatureScatter_scCustom", "title": "Modified version of FeatureScatter", "concept": [ "seurat_plotting" ], "topics": [ "FeatureScatter_scCustom" ] }, { "page": "Fetch_Meta", "title": "Get meta data from object", "concept": [ "get_set_util", "liger_object_util" ], "topics": [ "Fetch_Meta", "Fetch_Meta.liger", "Fetch_Meta.Seurat" ] }, { "page": "Find_Factor_Cor", "title": "Find Factor Correlations", "concept": [ "liger_object_util" ], "topics": [ "Find_Factor_Cor" ] }, { "page": "Get_Reference_LIGER", "title": "Get Reference Dataset", "concept": [ "liger_object_util" ], "topics": [ "Get_Reference_LIGER" ] }, { "page": "Hue_Pal", "title": "Hue_Pal", "concept": [ "palettes" ], "topics": [ "Hue_Pal" ] }, { "page": "Idents", "title": "Extract or set default identities from object", "concept": [ "liger_object_util" ], "topics": [ "Idents.liger", "Idents<-.liger" ] }, { "page": "ieg_gene_list", "title": "Immediate Early Gene (IEG) gene lists", "concept": [ "data" ], "topics": [ "ieg_gene_list" ] }, { "page": "Iterate_Barcode_Rank_Plot", "title": "Iterative Barcode Rank Plots", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Iterate_Barcode_Rank_Plot" ] }, { "page": "Iterate_Cluster_Highlight_Plot", "title": "Iterate Cluster Highlight Plot", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_Cluster_Highlight_Plot" ] }, { "page": "Iterate_DimPlot_bySample", "title": "Iterate DimPlot By Sample", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_DimPlot_bySample" ] }, { "page": "Iterate_FeaturePlot_scCustom", "title": "Iterative Plotting of Gene Lists using Custom FeaturePlots", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_FeaturePlot_scCustom" ] }, { "page": "Iterate_Meta_Highlight_Plot", "title": "Iterate Meta Highlight Plot", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_Meta_Highlight_Plot" ] }, { "page": "Iterate_PC_Loading_Plots", "title": "Iterate PC Loading Plots", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_PC_Loading_Plots" ] }, { "page": "Iterate_Plot_Density_Custom", "title": "Iterative Plotting of Gene Lists using Custom Density Plots", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_Plot_Density_Custom" ] }, { "page": "Iterate_Plot_Density_Joint", "title": "Iterative Plotting of Gene Lists using Custom Joint Density Plots", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_Plot_Density_Joint" ] }, { "page": "Iterate_VlnPlot_scCustom", "title": "Iterative Plotting of Gene Lists using VlnPlot_scCustom", "concept": [ "iterative_plotting" ], "topics": [ "Iterate_VlnPlot_scCustom" ] }, { "page": "JCO_Four", "title": "Four Color Palette (JCO)", "concept": [ "palettes" ], "topics": [ "JCO_Four" ] }, { "page": "lncRNA_gene_list", "title": "lncRNA gene list", "concept": [ "data" ], "topics": [ "lncRNA_gene_list" ] }, { "page": "MAD_Stats", "title": "Median Absolute Deviation Statistics", "concept": [ "stats" ], "topics": [ "MAD_Stats" ] }, { "page": "Map_New_Meta", "title": "Create new variable from categories in meta.data", "concept": [ "get_set_util" ], "topics": [ "Map_New_Meta" ] }, { "page": "Median_Stats", "title": "Median Statistics", "concept": [ "stats" ], "topics": [ "Median_Stats" ] }, { "page": "Merge_Seurat_List", "title": "Merge a list of Seurat Objects", "concept": [ "misc_util" ], "topics": [ "Merge_Seurat_List" ] }, { "page": "Merge_Sparse_Data_All", "title": "Merge a list of Sparse Matrices", "concept": [ "read_merge_util" ], "topics": [ "Merge_Sparse_Data_All" ] }, { "page": "Merge_Sparse_Multimodal_All", "title": "Merge a list of Sparse Matrices contain multi-modal data.", "concept": [ "read_merge_util" ], "topics": [ "Merge_Sparse_Multimodal_All" ] }, { "page": "Meta_Highlight_Plot", "title": "Meta Highlight Plot", "concept": [ "seurat_plotting" ], "topics": [ "Meta_Highlight_Plot" ] }, { "page": "Meta_Numeric", "title": "Check if meta data columns are numeric", "concept": [ "check_util" ], "topics": [ "Meta_Numeric" ] }, { "page": "Meta_Present", "title": "Check if meta data are present", "concept": [ "check_util" ], "topics": [ "Meta_Present" ] }, { "page": "Meta_Remove_Seurat", "title": "Remove meta data columns containing Seurat Defaults", "concept": [ "get_set_util" ], "topics": [ "Meta_Remove_Seurat" ] }, { "page": "Move_Legend", "title": "Move Legend Position", "concept": [ "themes" ], "topics": [ "Move_Legend" ] }, { "page": "msigdb_qc_ensembl_list", "title": "QC Gene Lists", "concept": [ "data" ], "topics": [ "msigdb_qc_ensembl_list" ] }, { "page": "msigdb_qc_gene_list", "title": "QC Gene Lists", "concept": [ "data" ], "topics": [ "msigdb_qc_gene_list" ] }, { "page": "NavyAndOrange", "title": "Navy and Orange Dual Color Palette", "concept": [ "palettes" ], "topics": [ "NavyAndOrange" ] }, { "page": "PalettePlot", "title": "Plot color palette in viewer", "concept": [ "palettes" ], "topics": [ "PalettePlot" ] }, { "page": "PC_Plotting", "title": "PC Plots", "concept": [ "seurat_plotting" ], "topics": [ "PC_Plotting" ] }, { "page": "Percent_Expressing", "title": "Calculate percent of expressing cells", "concept": [ "stats" ], "topics": [ "Percent_Expressing" ] }, { "page": "Plot_Cells_per_Sample", "title": "Plot Number of Cells/Nuclei per Sample", "concept": [ "stats_plotting" ], "topics": [ "Plot_Cells_per_Sample" ] }, { "page": "Plot_Density_Custom", "title": "Nebulosa Density Plot", "concept": [ "other_seurat_plotting" ], "topics": [ "Plot_Density_Custom" ] }, { "page": "Plot_Density_Joint_Only", "title": "Nebulosa Joint Density Plot", "concept": [ "other_seurat_plotting" ], "topics": [ "Plot_Density_Joint_Only" ] }, { "page": "Plot_Median_Genes", "title": "Plot Median Genes per Cell per Sample", "concept": [ "stats_plotting" ], "topics": [ "Plot_Median_Genes" ] }, { "page": "Plot_Median_Mito", "title": "Plot Median Percent Mito per Cell per Sample", "concept": [ "stats_plotting" ], "topics": [ "Plot_Median_Mito" ] }, { "page": "Plot_Median_Other", "title": "Plot Median other variable per Cell per Sample", "concept": [ "stats_plotting" ], "topics": [ "Plot_Median_Other" ] }, { "page": "Plot_Median_UMIs", "title": "Plot Median UMIs per Cell per Sample", "concept": [ "stats_plotting" ], "topics": [ "Plot_Median_UMIs" ] }, { "page": "plotFactors_scCustom", "title": "Customized version of plotFactors", "concept": [ "liger_plotting" ], "topics": [ "plotFactors_scCustom" ] }, { "page": "Proportion_Plot", "title": "Cell Proportion Plot", "concept": [ "stats_plotting" ], "topics": [ "Proportion_Plot" ] }, { "page": "Proportion_Plot_per_Sample", "title": "Cell Proportion Plot per Sample", "concept": [ "stats_plotting" ], "topics": [ "Proportion_Plot_per_Sample" ] }, { "page": "Pull_Cluster_Annotation", "title": "Pull cluster information from annotation csv file.", "concept": [ "marker_annotation_util" ], "topics": [ "Pull_Cluster_Annotation" ] }, { "page": "Pull_Directory_List", "title": "Pull Directory List", "concept": [ "read_&_write" ], "topics": [ "Pull_Directory_List" ] }, { "page": "QC_Histogram", "title": "QC Histogram Plots", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Histogram" ] }, { "page": "QC_Plot_GenevsFeature", "title": "QC Plots Genes vs Misc", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plot_GenevsFeature" ] }, { "page": "QC_Plot_UMIvsFeature", "title": "QC Plots UMI vs Misc", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plot_UMIvsFeature" ] }, { "page": "QC_Plot_UMIvsGene", "title": "QC Plots Genes vs UMIs", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plot_UMIvsGene" ] }, { "page": "QC_Plots_Combined_Vln", "title": "QC Plots Genes, UMIs, & % Mito", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_Combined_Vln" ] }, { "page": "QC_Plots_Complexity", "title": "QC Plots Cell \"Complexity\"", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_Complexity" ] }, { "page": "QC_Plots_Feature", "title": "QC Plots Feature", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_Feature" ] }, { "page": "QC_Plots_Genes", "title": "QC Plots Genes", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_Genes" ] }, { "page": "QC_Plots_Mito", "title": "QC Plots Mito", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_Mito" ] }, { "page": "QC_Plots_UMIs", "title": "QC Plots UMIs", "concept": [ "object_qc_plotting" ], "topics": [ "QC_Plots_UMIs" ] }, { "page": "Random_Cells_Downsample", "title": "Randomly downsample by identity", "concept": [ "get_set_util" ], "topics": [ "Random_Cells_Downsample" ] }, { "page": "Read_Add_cNMF", "title": "Read and add results from cNMF", "concept": [ "read_&_write" ], "topics": [ "Read_Add_cNMF" ] }, { "page": "Read_CellBender_h5_Mat", "title": "Load CellBender h5 matrices (corrected)", "concept": [ "read_&_write" ], "topics": [ "Read_CellBender_h5_Mat" ] }, { "page": "Read_CellBender_h5_Multi_Directory", "title": "Load CellBender h5 matrices (corrected) from multiple directories", "concept": [ "read_&_write" ], "topics": [ "Read_CellBender_h5_Multi_Directory" ] }, { "page": "Read_CellBender_h5_Multi_File", "title": "Load CellBender h5 matrices (corrected) from multiple files", "concept": [ "read_&_write" ], "topics": [ "Read_CellBender_h5_Multi_File" ] }, { "page": "Read_GEO_Delim", "title": "Load in NCBI GEO data formatted as single file per sample", "concept": [ "read_&_write" ], "topics": [ "Read_GEO_Delim" ] }, { "page": "Read_Metrics_10X", "title": "Read Overall Statistics from 10X Cell Ranger Count", "concept": [ "read_&_write" ], "topics": [ "Read_Metrics_10X" ] }, { "page": "Read_Metrics_CellBender", "title": "Read Overall Statistics from CellBender", "concept": [ "read_&_write" ], "topics": [ "Read_Metrics_CellBender" ] }, { "page": "Read_Velocity", "title": "Load RNA Velocity results", "concept": [ "read_&_write" ], "topics": [ "Read_Velocity" ] }, { "page": "Read10X_GEO", "title": "Load in NCBI GEO data from 10X", "concept": [ "read_&_write" ], "topics": [ "Read10X_GEO" ] }, { "page": "Read10X_h5_GEO", "title": "Load in NCBI GEO data from 10X in HDF5 file format", "concept": [ "read_&_write" ], "topics": [ "Read10X_h5_GEO" ] }, { "page": "Read10X_h5_Multi_Directory", "title": "Load 10X h5 count matrices from multiple directories", "concept": [ "read_&_write" ], "topics": [ "Read10X_h5_Multi_Directory" ] }, { "page": "Read10X_Multi_Directory", "title": "Load 10X count matrices from multiple directories", "concept": [ "read_&_write" ], "topics": [ "Read10X_Multi_Directory" ] }, { "page": "Reduction_Loading_Present", "title": "Check if reduction loadings are present", "concept": [ "check_util" ], "topics": [ "Reduction_Loading_Present" ] }, { "page": "ReFilter_SeuratObject", "title": "Re-filter Seurat object", "concept": [ "misc_util" ], "topics": [ "ReFilter_SeuratObject" ] }, { "page": "Rename_Clusters", "title": "Rename Clusters", "concept": [ "get_set_util", "marker_annotation_util" ], "topics": [ "Rename_Clusters", "Rename_Clusters.liger", "Rename_Clusters.Seurat" ] }, { "page": "Replace_Suffix", "title": "Replace barcode suffixes", "concept": [ "barcode_util" ], "topics": [ "Replace_Suffix" ] }, { "page": "scCustomize_Palette", "title": "Color Palette Selection for scCustomize", "concept": [ "palettes" ], "topics": [ "scCustomize_Palette" ] }, { "page": "Seq_QC_Plot_Alignment_Combined", "title": "QC Plots Sequencing metrics (Alignment) (Layout)", "concept": [ "seq_qc_plotting_layout" ], "topics": [ "Seq_QC_Plot_Alignment_Combined" ] }, { "page": "Seq_QC_Plot_Antisense", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Antisense" ] }, { "page": "Seq_QC_Plot_Basic_Combined", "title": "QC Plots Sequencing metrics (Layout)", "concept": [ "seq_qc_plotting_layout" ], "topics": [ "Seq_QC_Plot_Basic_Combined" ] }, { "page": "Seq_QC_Plot_Exonic", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Exonic" ] }, { "page": "Seq_QC_Plot_Genes", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Genes" ] }, { "page": "Seq_QC_Plot_Genome", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Genome" ] }, { "page": "Seq_QC_Plot_Intergenic", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Intergenic" ] }, { "page": "Seq_QC_Plot_Intronic", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Intronic" ] }, { "page": "Seq_QC_Plot_Number_Cells", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Number_Cells" ] }, { "page": "Seq_QC_Plot_Reads_in_Cells", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Reads_in_Cells" ] }, { "page": "Seq_QC_Plot_Reads_per_Cell", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Reads_per_Cell" ] }, { "page": "Seq_QC_Plot_Saturation", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Saturation" ] }, { "page": "Seq_QC_Plot_Total_Genes", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_Total_Genes" ] }, { "page": "Seq_QC_Plot_Transcriptome", "title": "QC Plots Sequencing metrics (Alignment)", "concept": [ "seq_qc_plotting_alignment" ], "topics": [ "Seq_QC_Plot_Transcriptome" ] }, { "page": "Seq_QC_Plot_UMIs", "title": "QC Plots Sequencing metrics", "concept": [ "seq_qc_plotting_basic" ], "topics": [ "Seq_QC_Plot_UMIs" ] }, { "page": "seq_zeros", "title": "Create sequence with zeros", "concept": [ "misc_util" ], "topics": [ "seq_zeros" ] }, { "page": "Setup_scRNAseq_Project", "title": "Setup project directory structure", "concept": [ "organization_util" ], "topics": [ "Setup_scRNAseq_Project" ] }, { "page": "Single_Color_Palette", "title": "Single Color Palettes for Plotting", "concept": [ "palettes" ], "topics": [ "Single_Color_Palette" ] }, { "page": "SpatialDimPlot_scCustom", "title": "SpatialDimPlot with modified default settings", "concept": [ "seurat_plotting" ], "topics": [ "SpatialDimPlot_scCustom" ] }, { "page": "Split_Layers", "title": "Split Seurat object into layers", "concept": [ "object_conversion" ], "topics": [ "Split_Layers" ] }, { "page": "Split_Vector", "title": "Split vector into list", "concept": [ "misc_util" ], "topics": [ "Split_Vector" ] }, { "page": "Stacked_VlnPlot", "title": "Stacked Violin Plot", "concept": [ "seurat_plotting" ], "topics": [ "Stacked_VlnPlot" ] }, { "page": "Store_Misc_Info_Seurat", "title": "Store misc data in Seurat object", "concept": [ "get_set_util" ], "topics": [ "Store_Misc_Info_Seurat" ] }, { "page": "Store_Palette_Seurat", "title": "Store color palette in Seurat object", "concept": [ "get_set_util" ], "topics": [ "Store_Palette_Seurat" ] }, { "page": "Subset_LIGER", "title": "Subset LIGER object", "concept": [ "liger_object_util" ], "topics": [ "Subset_LIGER" ] }, { "page": "theme_ggprism_mod", "title": "Modified ggprism theme", "concept": [ "themes" ], "topics": [ "theme_ggprism_mod" ] }, { "page": "Top_Genes_Factor", "title": "Extract top loading genes for LIGER factor", "concept": [ "liger_object_util", "marker_annotation_util" ], "topics": [ "Top_Genes_Factor", "Top_Genes_Factor.liger", "Top_Genes_Factor.Seurat" ] }, { "page": "UnRotate_X", "title": "Unrotate x axis on VlnPlot", "concept": [ "themes" ], "topics": [ "UnRotate_X" ] }, { "page": "Updated_HGNC_Symbols", "title": "Update HGNC Gene Symbols", "concept": [ "misc_util" ], "topics": [ "Updated_HGNC_Symbols" ] }, { "page": "Updated_MGI_Symbols", "title": "Update MGI Gene Symbols", "concept": [ "misc_util" ], "topics": [ "Updated_MGI_Symbols" ] }, { "page": "Variable_Features_ALL_LIGER", "title": "Perform variable gene selection over whole dataset", "concept": [ "liger_object_util" ], "topics": [ "Variable_Features_ALL_LIGER" ] }, { "page": "VariableFeaturePlot_scCustom", "title": "Custom Labeled Variable Features Plot", "concept": [ "seurat_plotting" ], "topics": [ "VariableFeaturePlot_scCustom" ] }, { "page": "viridis_shortcut", "title": "Viridis Shortcuts", "concept": [ "palettes" ], "topics": [ "viridis_dark_high", "viridis_inferno_dark_high", "viridis_inferno_light_high", "viridis_light_high", "viridis_magma_dark_high", "viridis_magma_light_high", "viridis_plasma_dark_high", "viridis_plasma_light_high" ] }, { "page": "VlnPlot_scCustom", "title": "VlnPlot with modified default settings", "concept": [ "seurat_plotting" ], "topics": [ "VlnPlot_scCustom" ] }, { "page": "WhichCells", "title": "Extract Cells for particular identity", "concept": [ 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