Files in scCustomize

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

NEWS.md README.md R/LIGER_Utilities.R R/Color_Palettes.R R/Statistics.R R/Plotting_Statistics.R R/Generics.R R/Plotting_Nebulosa.R R/Internal_Utilities.R R/LIGER_Plotting.R R/Utilities.R R/Plotting_QC_Seq_10X.R R/Read_&_Write_Data.R R/Plotting_Seurat_Iterative.R R/Object_Utilities.R R/Object_Conversion.R R/Data.R R/Deprecated.R R/zzz.R R/QC_Utilities_Seurat.R R/Plotting_Seurat.R R/Plotting_QC_Seurat.R R/LIGER_Internal_Utilities.R R/Reexports.R R/Plotting_Utilities.R man/ensembl_hemo_id.Rd man/Merge_Seurat_List.Rd man/Cluster_Highlight_Plot.Rd man/FeaturePlot_DualAssay.Rd man/Merge_Sparse_Data_All.Rd man/PC_Plotting.Rd man/Cell_Highlight_Plot.Rd man/Iterate_PC_Loading_Plots.Rd man/DimPlot_LIGER.Rd man/Random_Cells_Downsample.Rd man/Add_Mito_Ribo.Rd man/Meta_Present.Rd man/Read_Metrics_CellBender.Rd man/CellBender_Feature_Diff.Rd man/Split_Vector.Rd man/ensembl_ribo_id.Rd man/Read_CellBender_h5_Mat.Rd man/PalettePlot.Rd man/reexports.Rd man/MAD_Stats.Rd man/Read10X_GEO.Rd man/Embeddings.Rd man/FeaturePlot_scCustom.Rd man/Median_Stats.Rd man/Plot_Median_Mito.Rd man/Extract_Top_Markers.Rd man/Seq_QC_Plot_Antisense.Rd man/Add_Alt_Feature_ID.Rd man/Change_Delim_All.Rd man/msigdb_qc_gene_list.Rd man/QC_Plot_GenevsFeature.Rd man/Cells.Rd man/Read10X_h5_Multi_Directory.Rd man/Seq_QC_Plot_Genes.Rd man/Factor_Cor_Plot.Rd man/Seq_QC_Plot_Reads_in_Cells.Rd man/Read10X_Multi_Directory.Rd man/Plot_Density_Joint_Only.Rd man/Iterate_Barcode_Rank_Plot.Rd man/scCustomize_Palette.Rd man/Dark2_Pal.Rd man/Store_Palette_Seurat.Rd man/Features.Rd man/Add_Cell_QC_Metrics.Rd man/Copy_To_GCP.Rd man/SpatialDimPlot_scCustom.Rd man/Subset_LIGER.Rd man/QC_Plot_UMIvsFeature.Rd man/Add_Pct_Diff.Rd man/Read10X_h5_GEO.Rd man/Iterate_Meta_Highlight_Plot.Rd man/Case_Check.Rd man/Liger_to_Seurat.Rd man/QC_Plots_Genes.Rd man/QC_Plots_Complexity.Rd man/Create_CellBender_Merged_Seurat.Rd man/QC_Plot_UMIvsGene.Rd man/Cells_by_Identities_LIGER.Rd man/ieg_gene_list.Rd man/Add_Sample_Meta.Rd man/Plot_Cells_per_Sample.Rd man/Read_Metrics_10X.Rd man/Iterate_Cluster_Highlight_Plot.Rd man/Extract_Modality.Rd man/Rename_Clusters.Rd man/Move_Legend.Rd man/NavyAndOrange.Rd man/as.anndata.Rd man/Iterate_VlnPlot_scCustom.Rd man/Seq_QC_Plot_UMIs.Rd man/Extract_Sample_Meta.Rd man/Meta_Remove_Seurat.Rd man/UnRotate_X.Rd man/Seq_QC_Plot_Intergenic.Rd man/Variable_Features_ALL_LIGER.Rd man/Add_Cell_Complexity.Rd man/QC_Plots_Combined_Vln.Rd man/Seq_QC_Plot_Reads_per_Cell.Rd man/seq_zeros.Rd man/Iterate_FeaturePlot_scCustom.Rd man/Plot_Median_Genes.Rd man/Find_Factor_Cor.Rd man/FeatureScatter_scCustom.Rd man/Clustered_DotPlot.Rd man/Seq_QC_Plot_Intronic.Rd man/WhichCells.Rd man/Read_GEO_Delim.Rd man/DimPlot_scCustom.Rd man/Create_10X_H5.Rd man/Cells_per_Sample.Rd man/Cluster_Stats_All_Samples.Rd man/Idents.Rd man/Setup_scRNAseq_Project.Rd man/VlnPlot_scCustom.Rd man/QC_Plots_Feature.Rd man/Reduction_Loading_Present.Rd man/Meta_Numeric.Rd man/Store_Misc_Info_Seurat.Rd man/Seq_QC_Plot_Number_Cells.Rd man/Iterate_Plot_Density_Custom.Rd man/Seq_QC_Plot_Genome.Rd man/Plot_Median_UMIs.Rd man/as.Seurat.Rd man/Blank_Theme.Rd man/CheckMatrix_scCustom.Rd man/ensembl_ieg_list.Rd man/Updated_HGNC_Symbols.Rd man/QC_Plots_UMIs.Rd man/Add_CellBender_Diff.Rd man/Meta_Highlight_Plot.Rd man/QC_Histogram.Rd man/Seq_QC_Plot_Exonic.Rd man/Seq_QC_Plot_Basic_Combined.Rd man/Plot_Median_Other.Rd man/Seq_QC_Plot_Saturation.Rd man/Read_CellBender_h5_Multi_File.Rd man/scCustomize-package.Rd man/QC_Plots_Mito.Rd man/Proportion_Plot.Rd man/Merge_Sparse_Multimodal_All.Rd man/DimPlot_All_Samples.Rd man/VariableFeaturePlot_scCustom.Rd man/Add_Hemo.Rd man/CellBender_Diff_Plot.Rd man/theme_ggprism_mod.Rd man/Feature_Present.Rd man/Iterate_DimPlot_bySample.Rd man/Single_Color_Palette.Rd man/Split_Layers.Rd man/deprecated.Rd man/Updated_MGI_Symbols.Rd man/viridis_shortcut.Rd man/JCO_Four.Rd man/Seq_QC_Plot_Total_Genes.Rd man/as.LIGER.Rd man/Pull_Directory_List.Rd man/Plot_Density_Custom.Rd man/Iterate_Plot_Density_Joint.Rd man/Create_Cluster_Annotation_File.Rd man/Add_Top_Gene_Pct.Rd man/Change_Delim_Suffix.Rd man/Hue_Pal.Rd man/Pull_Cluster_Annotation.Rd man/Percent_Expressing.Rd man/Barcode_Plot.Rd man/Top_Genes_Factor.Rd man/Replace_Suffix.Rd man/Convert_Assay.Rd man/msigdb_qc_ensembl_list.Rd man/DiscretePalette_scCustomize.Rd man/plotFactors_scCustom.Rd man/ColorBlind_Pal.Rd man/Copy_From_GCP.Rd man/Change_Delim_Prefix.Rd man/ensembl_mito_id.Rd man/Stacked_VlnPlot.Rd man/Seq_QC_Plot_Transcriptome.Rd man/Fetch_Meta.Rd man/Seq_QC_Plot_Alignment_Combined.Rd man/DotPlot_scCustom.Rd man/Read_CellBender_h5_Multi_Directory.Rd