scCustomize2.1.2 package

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

DimPlot_All_Samples

DimPlot by Meta Data Column

Add_Alt_Feature_ID

Add Alternative Feature IDs

Add_Cell_Complexity

Add Cell Complexity

Add_Cell_QC_Metrics

Add Multiple Cell Quality Control Values with Single Function

Add_CellBender_Diff

Calculate and add differences post-cell bender analysis

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_Seurat

Add Percent of High Abundance Genes

as.anndata

Convert objects to anndata objects

as.LIGER

Convert objects to LIGER objects

as.Seurat

Convert objects to Seurat objects

Barcode_Plot

Create Barcode Rank Plot

Blank_Theme

Blank Theme

Case_Check

Check for alternate case features Checks Seurat object for the presenc...

Cell_Highlight_Plot

Meta Highlight Plot

CellBender_Diff_Plot

Plot Number of Cells/Nuclei per Sample

CellBender_Feature_Diff

CellBender Feature Differences

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

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

Feature_Present

Check if genes/features are present

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_Features

Extract Features from LIGER Object

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_Remove_Seurat

Remove meta data columns containing Seurat Defaults

Move_Legend

Move Legend Position

NavyAndOrange

Navy and Orange Dual Color Palette

PalettePlot

Plot color palette in viewer

PC_Plotting

PC Plots

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

plotFactors_scCustom

Customized version of plotFactors

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

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

Read10X_GEO

Load in NCBI GEO data from 10X

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

Read10X_Multi_Directory

Load 10X count matrices from multiple directories

Reduction_Loading_Present

Check if reduction loadings are present

reexports

Objects exported from other packages

Rename_Clusters

Rename Cluster Seurat

Replace_Suffix

Replace barcode suffixes

scCustomize-package

scCustomize: Custom Visualizations & Functions for Streamlined Analyse...

scCustomize_Palette

Color Palette Selection for scCustomize

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_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

theme_ggprism_mod

Modified ggprism theme

Top_Genes_Factor

Extract top loading genes for LIGER factor

UnRotate_X

Unrotate x axis on VlnPlot

Updated_HGNC_Symbols

Update HGNC Gene Symbols

Variable_Features_ALL_LIGER

Perform variable gene selection over whole dataset

VariableFeaturePlot_scCustom

Custom Labeled Variable Features Plot

viridis_shortcut

Viridis Shortcuts

VlnPlot_scCustom

VlnPlot with modified default settings

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

deprecated

Deprecated functions

Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.

  • Maintainer: Samuel Marsh
  • License: GPL (>= 3)
  • Last published: 2024-02-28