scCustomize
Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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Functions
473
Source code
24
Man pages
172
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scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
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API

API for scCustomize
Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Global functions
.get_bioc_cache Source code
.onAttach Source code
.onLoad Source code
Add_Alt_Feature_ID Man page Source code
Add_CellBender_Diff Man page Source code
Add_Cell_Complexity Man page Source code
Add_Cell_Complexity.Seurat Man page Source code
Add_Cell_Complexity.liger Man page Source code
Add_Cell_QC_Metrics Man page Source code
Add_Cell_QC_Metrics.Seurat Man page Source code
Add_Cell_QC_Metrics.liger Man page Source code
Add_Hemo Man page Source code
Add_Hemo.Seurat Man page Source code
Add_Hemo.liger Man page Source code
Add_IEG_LIGER Source code
Add_IEG_Seurat Source code
Add_MALAT1_Threshold Man page Source code
Add_MALAT1_Threshold.Seurat Man page Source code
Add_MSigDB_LIGER Source code
Add_MSigDB_Seurat Source code
Add_Mito_Ribo Man page Source code
Add_Mito_Ribo.Seurat Man page Source code
Add_Mito_Ribo.liger Man page Source code
Add_Pct_Diff Man page Source code
Add_Sample_Meta Man page Source code
Add_Top_Gene_Pct Man page Source code
Add_Top_Gene_Pct.Seurat Man page Source code
Add_Top_Gene_Pct.liger Man page Source code
Add_Top_Gene_Pct_Seurat Man page Source code
Add_lncRNA_LIGER Source code
Add_lncRNA_Seurat Source code
Assay5_Check Source code
Assay_Present Source code
AutoPointSize_scCustom Source code
Barcode_Plot Man page Source code
Blank_Theme Man page Source code
Case_Check Man page Source code
CellBender_Diff_Plot Man page Source code
CellBender_Feature_Diff Man page Source code
Cell_Highlight_Plot Man page Source code
Cells Man page
Cells.liger Man page Source code
Cells_by_Identities_LIGER Man page Source code
Cells_per_Sample Man page Source code
Change_Delim_All Man page Source code
Change_Delim_Prefix Man page Source code
Change_Delim_Suffix Man page Source code
CheckMatrix_scCustom Man page Source code
Check_Normalized Source code
Cluster_Annotation_Tibble Source code
Cluster_Highlight_Plot Man page Source code
Cluster_Stats_All_Samples Man page Source code
Clustered_DotPlot Man page Source code
Clustered_DotPlot_Multi_Group Source code
Clustered_DotPlot_Single_Group Source code
ColorBlind_Pal Man page Source code
Convert_Assay Man page Source code
Copy_From_GCP Man page Source code
Copy_To_GCP Man page Source code
Create_10X_H5 Man page Source code
Create_CellBender_Merged_Seurat Man page Source code
Create_Cluster_Annotation_File Man page Source code
Dark2_Pal Man page Source code
Dataset_Size_LIGER Man page Source code
Default_DimReduc_LIGER Source code
DimPlot_All_Samples Man page Source code
DimPlot_LIGER Man page Source code
DimPlot_scCustom Man page Source code
DiscretePalette_scCustomize Man page Source code
DotPlot_scCustom Man page Source code
Embeddings Man page
Embeddings.liger Man page Source code
ExtractField Source code
Extract_Max Source code
Extract_Modality Man page Source code
Extract_Sample_Meta Man page Source code
Extract_Top_Markers Man page Source code
Factor_Cor_Plot Man page Source code
FeaturePlot_DualAssay Man page Source code
FeaturePlot_scCustom Man page Source code
FeatureScatter_scCustom Man page Source code
Feature_PreCheck Source code
Feature_Present Man page Source code
Features Man page
Features.liger Man page Source code
Fetch_Meta Man page Source code
Fetch_Meta.Seurat Man page Source code
Fetch_Meta.liger Man page Source code
Figure_Plot Source code
Find_Factor_Cor Man page Source code
Generate_Plotting_df_LIGER Source code
Generate_Plotting_df_LIGER2 Source code
Get_Reference_LIGER Man page Source code
Hue_Pal Man page Source code
Idents Man page
Idents.liger Man page Source code
Idents<- Man page
Idents<-.liger Man page
Is_Color Source code
Is_LIGER Source code
Is_Seurat Source code
Iterate_Barcode_Rank_Plot Man page Source code
Iterate_Cluster_Highlight_Plot Man page Source code
Iterate_DimPlot_bySample Man page Source code
Iterate_FeaturePlot_scCustom Man page Source code
Iterate_Meta_Highlight_Plot Man page Source code
Iterate_PC_Loading_Plots Man page Source code
Iterate_Plot_Density_Custom Man page Source code
Iterate_Plot_Density_Joint Man page Source code
Iterate_VlnPlot_scCustom Man page Source code
JCO_Four Man page Source code
LIGER2_DimPlot Source code
LIGER_Default_Cluster_Name Source code
LIGER_DimPlot Source code
Liger_to_Seurat Man page Source code
MAD_Stats Man page Source code
Median_Stats Man page Source code
Merge_Seurat_List Man page Source code
Merge_Sparse_Data_All Man page Source code
Merge_Sparse_Multimodal_All Man page Source code
Meta_Highlight_Plot Man page Source code
Meta_Numeric Man page Source code
Meta_Present Man page Source code
Meta_Remove_Seurat Man page Source code
Metrics_Count_GEX Source code
Metrics_Count_GEX_v9plus Source code
Metrics_Multi_GEX Source code
Metrics_Multi_VDJT Source code
Metrics_Single_File Source code
Metrics_Single_File_v9plus Source code
Middle_Number Source code
Modify_VlnPlot Source code
Move_Legend Man page Source code
NavyAndOrange Man page Source code
No_Right Source code
Overall_Prop_Plot Source code
PC_Plotting Man page Source code
PalettePlot Man page Source code
PercentAbove_Seurat Source code
Percent_Expressing Man page Source code
Percent_Expressing_Meta Source code
Plot_Bar_Proportions Source code
Plot_By_Cluster_LIGER Source code
Plot_By_Cluster_LIGER2 Source code
Plot_By_Meta_LIGER Source code
Plot_By_Meta_LIGER2 Source code
Plot_Cells_per_Sample Man page Source code
Plot_Density_Custom Man page Source code
Plot_Density_Joint_Only Man page Source code
Plot_Median_Genes Man page Source code
Plot_Median_Mito Man page Source code
Plot_Median_Other Man page Source code
Plot_Median_UMIs Man page Source code
Plot_Pie_Proportions Source code
Proportion_Plot Man page Source code
Proportion_Plot_per_Sample Man page Source code
Pull_Cluster_Annotation Man page Source code
Pull_Directory_List Man page Source code
QC_Histogram Man page Source code
QC_Plot_GenevsFeature Man page Source code
QC_Plot_UMIvsFeature Man page Source code
QC_Plot_UMIvsGene Man page Source code
QC_Plots_Combined_Vln Man page Source code
QC_Plots_Complexity Man page Source code
QC_Plots_Feature Man page Source code
QC_Plots_Genes Man page Source code
QC_Plots_Mito Man page Source code
QC_Plots_UMIs Man page Source code
Random_Cells_Downsample Man page Source code
Read10X_GEO Man page Source code
Read10X_Multi_Directory Man page Source code
Read10X_h5_GEO Man page Source code
Read10X_h5_Multi_Directory Man page Source code
Read_Add_cNMF Man page Source code
Read_CellBender_h5_Mat Man page Source code
Read_CellBender_h5_Multi_Directory Man page Source code
Read_CellBender_h5_Multi_File Man page Source code
Read_GEO_Delim Man page Source code
Read_Metrics_10X Man page Source code
Read_Metrics_CellBender Man page Source code
Reduction_Loading_Present Man page Source code
Rename_Clusters Man page Source code
Rename_Clusters.Seurat Man page Source code
Rename_Clusters.liger Man page Source code
Replace_Suffix Man page Source code
Retrieve_Dual_Mito_Features Source code
Retrieve_Dual_Ribo_Features Source code
Retrieve_Ensembl_Hemo Source code
Retrieve_Ensembl_Mito Source code
Retrieve_Ensembl_Ribo Source code
Retrieve_Ensembl_lncRNA Source code
Retrieve_IEG_Ensembl_Lists Source code
Retrieve_IEG_Lists Source code
Retrieve_MALAT1_Ensembl_Lists Source code
Retrieve_MSigDB_Ensembl_Lists Source code
Retrieve_MSigDB_Lists Source code
Retrieve_exAM_Ensembl_Lists Source code
Retrieve_exAM_Lists Source code
Retrieve_lncRNA Source code
Return_QC_Defaults Source code
Seq_QC_Plot_Alignment_Combined Man page Source code
Seq_QC_Plot_Antisense Man page Source code
Seq_QC_Plot_Basic_Combined Man page Source code
Seq_QC_Plot_Exonic Man page Source code
Seq_QC_Plot_Genes Man page Source code
Seq_QC_Plot_Genome Man page Source code
Seq_QC_Plot_Intergenic Man page Source code
Seq_QC_Plot_Intronic Man page Source code
Seq_QC_Plot_Number_Cells Man page Source code
Seq_QC_Plot_Reads_in_Cells Man page Source code
Seq_QC_Plot_Reads_per_Cell Man page Source code
Seq_QC_Plot_Saturation Man page Source code
Seq_QC_Plot_Total_Genes Man page Source code
Seq_QC_Plot_Transcriptome Man page Source code
Seq_QC_Plot_UMIs Man page Source code
Setup_scRNAseq_Project Man page Source code
Single_Color_Palette Man page Source code
SpatialDimPlot_scCustom Man page Source code
Split_Layers Man page Source code
Split_Vector Man page Source code
Stacked_VlnPlot Man page Source code
Store_Misc_Info_Seurat Man page Source code
Store_Palette_Seurat Man page Source code
Subset_LIGER Man page Source code
Test_Integer Source code
Top_Genes_Factor Man page Source code
Top_Genes_Factor.Seurat Man page Source code
Top_Genes_Factor.liger Man page Source code
UnRotate_X Man page Source code
Updated_HGNC_Symbols Man page Source code
Updated_MGI_Symbols Man page Source code
VariableFeaturePlot_scCustom Man page Source code
Variable_Features_ALL_LIGER Man page Source code
VlnPlot_scCustom Man page Source code
WhichCells Man page
WhichCells.liger Man page Source code
`%iff%` Source code
`%||%` Source code
as.LIGER Man page Source code
as.LIGER.Seurat Man page Source code
as.LIGER.list Man page Source code
as.Seurat Man page
as.Seurat.liger Man page Source code
as.anndata Man page Source code
as.anndata.Seurat Man page Source code
as.anndata.liger Man page Source code
check_extension Source code
check_whole_num Source code
create_factor_hclust_rect Source code
define_malat1_threshold Source code
download_hgnc_data Source code
download_mgi_data Source code
drop_single_value_cols Source code
ensembl_exAM_list Man page
ensembl_hemo_id Man page
ensembl_ieg_list Man page
ensembl_lncRNA_id Man page
ensembl_malat1_list Man page
ensembl_mito_id Man page
ensembl_ribo_id Man page
exAM_Scoring Man page Source code
exAM_gene_list Man page
glue_collapse_scCustom Source code
ieg_gene_list Man page
kMeans_Elbow Source code
lncRNA_gene_list Man page
lower_diag_cor_mat Source code
msigdb_qc_ensembl_list Man page
msigdb_qc_gene_list Man page
plotFactors_liger2_scCustom Source code
plotFactors_liger_scCustom Source code
plotFactors_scCustom Man page Source code
process_hgnc_data Source code
process_mgi_data Source code
reexports Man page
replace_null Source code
scCustomize Man page
scCustomize-package Man page
scCustomize_Palette Man page Source code
scCustomze_Split_FeatureScatter Source code
seq_zeros Man page Source code
stop_quietly Source code
symdiff Source code
theme_ggprism_mod Man page Source code
upper_diag_cor_mat Source code
varibow_scCustom Source code
viridis_dark_high Man page
viridis_inferno_dark_high Man page
viridis_inferno_light_high Man page
viridis_light_high Man page
viridis_magma_dark_high Man page
viridis_magma_light_high Man page
viridis_plasma_dark_high Man page
viridis_plasma_light_high Man page
yesno Source code
scCustomize documentation built on Aug. 26, 2025, 9:08 a.m.

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