scCustomize3.0.1 package

Add Alternative Feature IDs

Add Cell Complexity

Add Multiple Cell Quality Control Values with Single Function

Calculate and add differences post-cell bender analysis

Add Hemoglobin percentages

Add Mito and Ribo percentages

Add percentage difference to DE results

Add Sample Level Meta Data

Add Percent of High Abundance Genes

Convert objects to anndata objects

Convert objects to LIGER objects

Convert objects to Seurat objects

Create Barcode Rank Plot

Blank Theme

Check for alternate case features

Meta Highlight Plot

Plot Number of Cells/Nuclei per Sample

CellBender Feature Differences

Extract Cells by identity

Cells per Sample

Extract Cells from LIGER Object

Change all delimiters in cell name

Change barcode prefix delimiter

Change barcode suffix delimiter

Check Matrix Validity

Cluster Highlight Plot

Calculate Cluster Stats

Clustered DotPlot

Color Universal Design Short Palette

Convert between Seurat Assay types

Copy folder from GCP bucket from R Console

Copy folder to GCP bucket from R Console

Create H5 from 10X Outputs

Create Seurat Object with Cell Bender and Raw data

Create cluster annotation csv file

Dark2 Palette

Deprecated functions

DimPlot by Meta Data Column

DimPlot LIGER Version

DimPlot with modified default settings

Discrete color palettes

Customized DotPlot

Extract matrix of embeddings

Extract multi-modal data into list by modality

Extract sample level meta.data

Extract Top N Marker Genes

Factor Correlation Plot

Check if genes/features are present

Customize FeaturePlot of two assays

Customize FeaturePlot

Extract Features from LIGER Object

Modified version of FeatureScatter

Get meta data from object

Find Factor Correlations

Hue_Pal

Extract or set default identities from object

Iterative Barcode Rank Plots

Iterate Cluster Highlight Plot

Iterate DimPlot By Sample

Iterative Plotting of Gene Lists using Custom FeaturePlots

Iterate Meta Highlight Plot

Iterate PC Loading Plots

Iterative Plotting of Gene Lists using Custom Density Plots

Iterative Plotting of Gene Lists using Custom Joint Density Plots

Iterative Plotting of Gene Lists using VlnPlot_scCustom

Four Color Palette (JCO)

Create a Seurat object containing the data from a liger object

Median Absolute Deviation Statistics

Median Statistics

Merge a list of Seurat Objects

Merge a list of Sparse Matrices

Merge a list of Sparse Matrices contain multi-modal data.

Meta Highlight Plot

Check if meta data columns are numeric

Check if meta data are present

Remove meta data columns containing Seurat Defaults

Move Legend Position

Navy and Orange Dual Color Palette

Plot color palette in viewer

PC Plots

Calculate percent of expressing cells

Plot Number of Cells/Nuclei per Sample

Nebulosa Density Plot

Nebulosa Joint Density Plot

Plot Median Genes per Cell per Sample

Plot Median Percent Mito per Cell per Sample

Plot Median other variable per Cell per Sample

Plot Median UMIs per Cell per Sample

Customized version of plotFactors

Cell Proportion Plot

Pull cluster information from annotation csv file.

Pull Directory List

QC Histogram Plots

QC Plots Genes vs Misc

QC Plots UMI vs Misc

QC Plots Genes vs UMIs

QC Plots Genes, UMIs, & % Mito

QC Plots Cell "Complexity"

QC Plots Feature

QC Plots Genes

QC Plots Mito

QC Plots UMIs

Randomly downsample by identity

Load CellBender h5 matrices (corrected)

Load CellBender h5 matrices (corrected) from multiple directories

Load CellBender h5 matrices (corrected) from multiple files

Load in NCBI GEO data formatted as single file per sample

Read Overall Statistics from 10X Cell Ranger Count

Read Overall Statistics from CellBender

Load in NCBI GEO data from 10X

Load in NCBI GEO data from 10X in HDF5 file format

Load 10X h5 count matrices from multiple directories

Load 10X count matrices from multiple directories

Check if reduction loadings are present

Objects exported from other packages

Rename Clusters

Replace barcode suffixes

Color Palette Selection for scCustomize

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

QC Plots Sequencing metrics (Alignment) (Layout)

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics (Layout)

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics

QC Plots Sequencing metrics

QC Plots Sequencing metrics

QC Plots Sequencing metrics

QC Plots Sequencing metrics

QC Plots Sequencing metrics (Alignment)

QC Plots Sequencing metrics

Create sequence with zeros

Setup project directory structure

Single Color Palettes for Plotting

SpatialDimPlot with modified default settings

Split Seurat object into layers

Split vector into list

Stacked Violin Plot

Store misc data in Seurat object

Store color palette in Seurat object

Subset LIGER object

Modified ggprism theme

Extract top loading genes for LIGER factor

Unrotate x axis on VlnPlot

Update HGNC Gene Symbols

Update MGI Gene Symbols

Perform variable gene selection over whole dataset

Custom Labeled Variable Features Plot

Viridis Shortcuts

VlnPlot with modified default settings

Extract Cells for particular identity