scCustomize-package	scCustomize-package
Add_Alt_Feature_ID	Add_Alt_Feature_ID
Add_CellBender_Diff	Add_CellBender_Diff
Add_Cell_Complexity	Add_Cell_Complexity
Add_Cell_Complexity.liger	Add_Cell_Complexity
Add_Cell_Complexity.Seurat	Add_Cell_Complexity
Add_Cell_QC_Metrics	Add_Cell_QC_Metrics
Add_Cell_QC_Metrics.liger	Add_Cell_QC_Metrics
Add_Cell_QC_Metrics.Seurat	Add_Cell_QC_Metrics
Add_Hemo	Add_Hemo
Add_Hemo.liger	Add_Hemo
Add_Hemo.Seurat	Add_Hemo
Add_MALAT1_Threshold	Add_MALAT1_Threshold
Add_MALAT1_Threshold.Seurat	Add_MALAT1_Threshold
Add_Mito_Ribo	Add_Mito_Ribo
Add_Mito_Ribo.liger	Add_Mito_Ribo
Add_Mito_Ribo.Seurat	Add_Mito_Ribo
Add_Pct_Diff	Add_Pct_Diff
Add_Sample_Meta	Add_Sample_Meta
Add_Top_Gene_Pct	Add_Top_Gene_Pct
Add_Top_Gene_Pct.liger	Add_Top_Gene_Pct
Add_Top_Gene_Pct.Seurat	Add_Top_Gene_Pct
Add_Top_Gene_Pct_Seurat	deprecated
as.anndata	as.anndata
as.anndata.liger	as.anndata
as.anndata.Seurat	as.anndata
as.LIGER	as.LIGER
as.LIGER.list	as.LIGER
as.LIGER.Seurat	as.LIGER
as.Seurat	reexports
as.Seurat.liger	as.Seurat
Barcode_Plot	Barcode_Plot
Blank_Theme	Blank_Theme
Case_Check	Case_Check
CellBender_Diff_Plot	CellBender_Diff_Plot
CellBender_Feature_Diff	CellBender_Feature_Diff
Cells	reexports
Cells.liger	Cells
Cells_by_Identities_LIGER	Cells_by_Identities_LIGER
Cells_per_Sample	Cells_per_Sample
Cell_Highlight_Plot	Cell_Highlight_Plot
Change_Delim_All	Change_Delim_All
Change_Delim_Prefix	Change_Delim_Prefix
Change_Delim_Suffix	Change_Delim_Suffix
CheckMatrix_scCustom	CheckMatrix_scCustom
Clustered_DotPlot	Clustered_DotPlot
Cluster_Highlight_Plot	Cluster_Highlight_Plot
Cluster_Stats_All_Samples	Cluster_Stats_All_Samples
ColorBlind_Pal	ColorBlind_Pal
Convert_Assay	Convert_Assay
Copy_From_GCP	Copy_From_GCP
Copy_To_GCP	Copy_To_GCP
Create_10X_H5	Create_10X_H5
Create_CellBender_Merged_Seurat	Create_CellBender_Merged_Seurat
Create_Cluster_Annotation_File	Create_Cluster_Annotation_File
Dark2_Pal	Dark2_Pal
Dataset_Size_LIGER	Dataset_Size_LIGER
DimPlot_All_Samples	DimPlot_All_Samples
DimPlot_LIGER	DimPlot_LIGER
DimPlot_scCustom	DimPlot_scCustom
DiscretePalette_scCustomize	DiscretePalette_scCustomize
DotPlot_scCustom	DotPlot_scCustom
Embeddings	reexports
Embeddings.liger	Embeddings
ensembl_exAM_list	ensembl_exAM_list
ensembl_hemo_id	ensembl_hemo_id
ensembl_ieg_list	ensembl_ieg_list
ensembl_lncRNA_id	ensembl_lncRNA_id
ensembl_malat1_list	ensembl_malat1_list
ensembl_mito_id	ensembl_mito_id
ensembl_ribo_id	ensembl_ribo_id
exAM_gene_list	exAM_gene_list
exAM_Scoring	exAM_Scoring
Extract_Modality	Extract_Modality
Extract_Sample_Meta	Extract_Sample_Meta
Extract_Top_Markers	Extract_Top_Markers
Factor_Cor_Plot	Factor_Cor_Plot
FeaturePlot_DualAssay	FeaturePlot_DualAssay
FeaturePlot_scCustom	FeaturePlot_scCustom
Features	reexports
Features.liger	Features
FeatureScatter_scCustom	FeatureScatter_scCustom
Feature_Present	Feature_Present
Fetch_Meta	Fetch_Meta
Fetch_Meta.liger	Fetch_Meta
Fetch_Meta.Seurat	Fetch_Meta
Find_Factor_Cor	Find_Factor_Cor
Get_Reference_LIGER	Get_Reference_LIGER
Hue_Pal	Hue_Pal
Idents	reexports
Idents.liger	Idents
Idents<-	reexports
Idents<-.liger	Idents
ieg_gene_list	ieg_gene_list
Iterate_Barcode_Rank_Plot	Iterate_Barcode_Rank_Plot
Iterate_Cluster_Highlight_Plot	Iterate_Cluster_Highlight_Plot
Iterate_DimPlot_bySample	Iterate_DimPlot_bySample
Iterate_FeaturePlot_scCustom	Iterate_FeaturePlot_scCustom
Iterate_Meta_Highlight_Plot	Iterate_Meta_Highlight_Plot
Iterate_PC_Loading_Plots	Iterate_PC_Loading_Plots
Iterate_Plot_Density_Custom	Iterate_Plot_Density_Custom
Iterate_Plot_Density_Joint	Iterate_Plot_Density_Joint
Iterate_VlnPlot_scCustom	Iterate_VlnPlot_scCustom
JCO_Four	JCO_Four
Liger_to_Seurat	Liger_to_Seurat
lncRNA_gene_list	lncRNA_gene_list
MAD_Stats	MAD_Stats
Median_Stats	Median_Stats
Merge_Seurat_List	Merge_Seurat_List
Merge_Sparse_Data_All	Merge_Sparse_Data_All
Merge_Sparse_Multimodal_All	Merge_Sparse_Multimodal_All
Meta_Highlight_Plot	Meta_Highlight_Plot
Meta_Numeric	Meta_Numeric
Meta_Present	Meta_Present
Meta_Remove_Seurat	Meta_Remove_Seurat
Move_Legend	Move_Legend
msigdb_qc_ensembl_list	msigdb_qc_ensembl_list
msigdb_qc_gene_list	msigdb_qc_gene_list
NavyAndOrange	NavyAndOrange
PalettePlot	PalettePlot
PC_Plotting	PC_Plotting
Percent_Expressing	Percent_Expressing
plotFactors_scCustom	plotFactors_scCustom
Plot_Cells_per_Sample	Plot_Cells_per_Sample
Plot_Density_Custom	Plot_Density_Custom
Plot_Density_Joint_Only	Plot_Density_Joint_Only
Plot_Median_Genes	Plot_Median_Genes
Plot_Median_Mito	Plot_Median_Mito
Plot_Median_Other	Plot_Median_Other
Plot_Median_UMIs	Plot_Median_UMIs
Proportion_Plot	Proportion_Plot
Proportion_Plot_per_Sample	Proportion_Plot_per_Sample
Pull_Cluster_Annotation	Pull_Cluster_Annotation
Pull_Directory_List	Pull_Directory_List
QC_Histogram	QC_Histogram
QC_Plots_Combined_Vln	QC_Plots_Combined_Vln
QC_Plots_Complexity	QC_Plots_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_GenevsFeature	QC_Plot_GenevsFeature
QC_Plot_UMIvsFeature	QC_Plot_UMIvsFeature
QC_Plot_UMIvsGene	QC_Plot_UMIvsGene
Random_Cells_Downsample	Random_Cells_Downsample
Read10X_GEO	Read10X_GEO
Read10X_h5_GEO	Read10X_h5_GEO
Read10X_h5_Multi_Directory	Read10X_h5_Multi_Directory
Read10X_Multi_Directory	Read10X_Multi_Directory
Read_Add_cNMF	Read_Add_cNMF
Read_CellBender_h5_Mat	Read_CellBender_h5_Mat
Read_CellBender_h5_Multi_Directory	Read_CellBender_h5_Multi_Directory
Read_CellBender_h5_Multi_File	Read_CellBender_h5_Multi_File
Read_GEO_Delim	Read_GEO_Delim
Read_Metrics_10X	Read_Metrics_10X
Read_Metrics_CellBender	Read_Metrics_CellBender
Reduction_Loading_Present	Reduction_Loading_Present
reexports	reexports
ReFilter_SeuratObject	ReFilter_SeuratObject
Rename_Clusters	Rename_Clusters
Rename_Clusters.liger	Rename_Clusters
Rename_Clusters.Seurat	Rename_Clusters
Replace_Suffix	Replace_Suffix
scCustomize	scCustomize-package
scCustomize_Palette	scCustomize_Palette
Seq_QC_Plot_Alignment_Combined	Seq_QC_Plot_Alignment_Combined
Seq_QC_Plot_Antisense	Seq_QC_Plot_Antisense
Seq_QC_Plot_Basic_Combined	Seq_QC_Plot_Basic_Combined
Seq_QC_Plot_Exonic	Seq_QC_Plot_Exonic
Seq_QC_Plot_Genes	Seq_QC_Plot_Genes
Seq_QC_Plot_Genome	Seq_QC_Plot_Genome
Seq_QC_Plot_Intergenic	Seq_QC_Plot_Intergenic
Seq_QC_Plot_Intronic	Seq_QC_Plot_Intronic
Seq_QC_Plot_Number_Cells	Seq_QC_Plot_Number_Cells
Seq_QC_Plot_Reads_in_Cells	Seq_QC_Plot_Reads_in_Cells
Seq_QC_Plot_Reads_per_Cell	Seq_QC_Plot_Reads_per_Cell
Seq_QC_Plot_Saturation	Seq_QC_Plot_Saturation
Seq_QC_Plot_Total_Genes	Seq_QC_Plot_Total_Genes
Seq_QC_Plot_Transcriptome	Seq_QC_Plot_Transcriptome
Seq_QC_Plot_UMIs	Seq_QC_Plot_UMIs
seq_zeros	seq_zeros
Setup_scRNAseq_Project	Setup_scRNAseq_Project
Single_Color_Palette	Single_Color_Palette
SpatialDimPlot_scCustom	SpatialDimPlot_scCustom
Split_Layers	Split_Layers
Split_Vector	Split_Vector
Stacked_VlnPlot	Stacked_VlnPlot
Store_Misc_Info_Seurat	Store_Misc_Info_Seurat
Store_Palette_Seurat	Store_Palette_Seurat
Subset_LIGER	Subset_LIGER
theme_ggprism_mod	theme_ggprism_mod
Top_Genes_Factor	Top_Genes_Factor
Top_Genes_Factor.liger	Top_Genes_Factor
Top_Genes_Factor.Seurat	Top_Genes_Factor
UnRotate_X	UnRotate_X
Updated_HGNC_Symbols	Updated_HGNC_Symbols
Updated_MGI_Symbols	Updated_MGI_Symbols
VariableFeaturePlot_scCustom	VariableFeaturePlot_scCustom
Variable_Features_ALL_LIGER	Variable_Features_ALL_LIGER
viridis_dark_high	viridis_shortcut
viridis_inferno_dark_high	viridis_shortcut
viridis_inferno_light_high	viridis_shortcut
viridis_light_high	viridis_shortcut
viridis_magma_dark_high	viridis_shortcut
viridis_magma_light_high	viridis_shortcut
viridis_plasma_dark_high	viridis_shortcut
viridis_plasma_light_high	viridis_shortcut
VlnPlot_scCustom	VlnPlot_scCustom
WhichCells	reexports
WhichCells.liger	WhichCells
