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_Cell_QC_Metrics     Add Multiple Cell Quality Control Values with
                        Single Function
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
Add_Top_Gene_Pct_Seurat
                        Add Percent of High Abundance Genes
Barcode_Plot            Create Barcode Rank Plot
Blank_Theme             Blank Theme
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
Cluster_Highlight_Plot
                        Cluster Highlight Plot
Cluster_Stats_All_Samples
                        Calculate Cluster Stats
Clustered_DotPlot       Clustered DotPlot
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
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
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
FeaturePlot_DualAssay   Customize FeaturePlot of two assays
FeaturePlot_scCustom    Customize FeaturePlot
FeatureScatter_scCustom
                        Modified version of FeatureScatter
Fetch_Meta              Get meta data from object
Gene_Present            Check if genes/features are present
Hue_Pal                 Hue_Pal
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 Plots
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 object
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_Present_LIGER      Check if meta data are present
Meta_Remove_Seurat      Remove meta data columns containing Seurat
                        Defaults
Move_Legend             Move Legend Position
NavyAndOrange           Navy and Orange Dual Color Palette
PC_Plotting             PC Plots
PalettePlot             Plot color palette in viewer
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
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
QC_Histogram            QC Histogram Plots
QC_Plot_GenevsFeature   QC Plots Genes vs Misc
QC_Plot_UMIvsFeature    QC Plots UMI vs Misc
QC_Plot_UMIvsGene       QC Plots Genes vs UMIs
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
Read10X_GEO             Load in NCBI GEO data from 10X
Read10X_Multi_Directory
                        Load 10X count matrices from multiple
                        directories
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
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
Reduction_Loading_Present
                        Check if reduction loadings are present
Rename_Clusters         Rename Cluster Seurat
Replace_Suffix          Replace barcode suffixes
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
Top_Genes_Factor        Extract top loading genes for LIGER factor
UnRotate_X              Unrotate x axis on VlnPlot
VariableFeaturePlot_scCustom
                        Custom Labeled Variable Features Plot
Variable_Features_ALL_LIGER
                        Perform variable gene selection over whole
                        dataset
VlnPlot_scCustom        VlnPlot with modified default settings
ensembl_mito_id         Ensembl Mito IDs
ensembl_ribo_id         Ensembl Ribo IDs
ieg_gene_list           Immediate Early Gene (IEG) gene lists
msigdb_qc_gene_list     QC Gene Lists
plotFactors_scCustom    Customized version of plotFactors
scCustomize_Palette     Color Palette Selection for scCustomize
theme_ggprism_mod       Modified ggprism theme
viridis_plasma_dark_high
                        Viridis Shortcuts
