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_MALAT1_Threshold    Add MALAT1 QC Threshold
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
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.liger             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
Cluster_Highlight_Plot
                        Cluster Highlight Plot
Cluster_Stats_All_Samples
                        Calculate Cluster Stats
Clustered_DotPlot       Clustered DotPlot
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
Dataset_Size_LIGER      Check size of LIGER datasets
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
ElbowPlot_scCustom      ElbowPlot with modifications
Embeddings.liger        Extract matrix of embeddings
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
FeatureScatter_scCustom
                        Modified version of FeatureScatter
Feature_Present         Check if genes/features are present
Features.liger          Extract Features from LIGER Object
Fetch_Meta              Get meta data from object
Find_Factor_Cor         Find Factor Correlations
Get_Reference_LIGER     Get Reference Dataset
Hue_Pal                 Hue_Pal
Idents.liger            Extract or set default identities from object
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)
MAD_Stats               Median Absolute Deviation Statistics
Map_New_Meta            Create new variable from categories in
                        meta.data
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
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
Proportion_Plot         Cell Proportion Plot
Proportion_Plot_per_Sample
                        Cell Proportion Plot 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
Random_Cells_Downsample
                        Randomly downsample by identity
ReFilter_SeuratObject   Re-filter Seurat object
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_Add_cNMF           Read and add results from cNMF
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
Read_Metrics_CellBender
                        Read Overall Statistics from CellBender
Reduction_Loading_Present
                        Check if reduction loadings are present
Rename_Clusters         Rename Clusters
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
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
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
VlnPlot_scCustom        VlnPlot with modified default settings
WhichCells.liger        Extract Cells for particular identity
as.LIGER                Convert objects to LIGER objects
as.Seurat.liger         Convert objects to 'Seurat' objects
as.anndata              Convert objects to anndata objects
ensembl_exAM_list       Immediate Early Gene (IEG) gene lists
ensembl_hemo_id         Ensembl Hemo IDs
ensembl_ieg_list        Immediate Early Gene (IEG) gene lists
ensembl_lncRNA_id       Ensembl lncRNA IDs
ensembl_malat1_list     MALAT1 gene lists
ensembl_mito_id         Ensembl Mito IDs
ensembl_ribo_id         Ensembl Ribo IDs
exAM_Scoring            Add exAM Gene List Module Scores
exAM_gene_list          exAM gene lists
ieg_gene_list           Immediate Early Gene (IEG) gene lists
lncRNA_gene_list        lncRNA gene list
msigdb_qc_ensembl_list
                        QC Gene Lists
msigdb_qc_gene_list     QC Gene Lists
plotFactors_scCustom    Customized version of plotFactors
scCustomize_Palette     Color Palette Selection for scCustomize
seq_zeros               Create sequence with zeros
theme_ggprism_mod       Modified ggprism theme
viridis_plasma_dark_high
                        Viridis Shortcuts
