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scCustomize  

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
View on CRAN: Click here


Download and install scCustomize package within the R console
Install from CRAN:
install.packages("scCustomize")

Install from Github:
library("remotes")
install_github("cran/scCustomize")

Install by package version:
library("remotes")
install_version("scCustomize", "3.0.1")



Attach the package and use:
library("scCustomize")
Maintained by
Samuel Marsh
[Scholar Profile | Author Map]
First Published: 2022-12-23
Latest Update: 2024-02-28
Description:
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" RRID:SCR_024675.
How to cite:
Samuel Marsh (2022). scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing. R package version 3.0.1, https://cran.r-project.org/web/packages/scCustomize. Accessed 29 Mar. 2025.
Previous versions and publish date:
1.1.0 (2022-12-23 20:10), 1.1.1 (2023-01-13 16:30), 1.1.2 (2023-07-18 23:50), 1.1.3 (2023-07-19 23:40), 2.0.0 (2023-11-14 06:40), 2.0.1 (2023-11-17 20:00), 2.1.0 (2024-02-23 20:40), 2.1.1 (2024-02-24 10:50), 2.1.2 (2024-02-28 20:40), 3.0.0 (2024-12-05 21:30)
Other packages that cited scCustomize R package
View scCustomize citation profile
Other R packages that scCustomize depends, imports, suggests or enhances
Complete documentation for scCustomize
Functions, R codes and Examples using the scCustomize R package
Some associated functions: Add_CellBender_Diff . Add_Cell_Complexity_LIGER . Add_Cell_Complexity_Seurat . Add_Cell_QC_Metrics . Add_Mito_Ribo_LIGER . Add_Mito_Ribo_Seurat . Add_Pct_Diff . Add_Sample_Meta . Add_Top_Gene_Pct_Seurat . Barcode_Plot . Blank_Theme . Case_Check . CellBender_Diff_Plot . CellBender_Feature_Diff . Cell_Highlight_Plot . Change_Delim_All . Change_Delim_Prefix . Change_Delim_Suffix . CheckMatrix_scCustom . Cluster_Highlight_Plot . Cluster_Stats_All_Samples . Clustered_DotPlot . ColorBlind_Pal . Copy_From_GCP . Copy_To_GCP . Create_10X_H5 . Create_CellBender_Merged_Seurat . Create_Cluster_Annotation_File . Dark2_Pal . DimPlot_All_Samples . DimPlot_LIGER . DimPlot_scCustom . DiscretePalette_scCustomize . DotPlot_scCustom . Extract_Modality . Extract_Sample_Meta . Extract_Top_Markers . FeaturePlot_DualAssay . FeaturePlot_scCustom . FeatureScatter_scCustom . Fetch_Meta . Gene_Present . Hue_Pal . Iterate_Barcode_Rank_Plot . Iterate_Cluster_Highlight_Plot . Iterate_DimPlot_bySample . Iterate_FeaturePlot_scCustom . Iterate_Meta_Highlight_Plot . Iterate_PC_Loading_Plots . Iterate_Plot_Density_Custom . Iterate_Plot_Density_Joint . Iterate_VlnPlot_scCustom . JCO_Four . Liger_to_Seurat . MAD_Stats . Median_Stats . Merge_Seurat_List . Merge_Sparse_Data_All . Merge_Sparse_Multimodal_All . Meta_Highlight_Plot . Meta_Numeric . Meta_Present . Meta_Present_LIGER . Meta_Remove_Seurat . Move_Legend . NavyAndOrange . PC_Plotting . PalettePlot . Percent_Expressing . Plot_Cells_per_Sample . Plot_Density_Custom . Plot_Density_Joint_Only . Plot_Median_Genes . Plot_Median_Mito . Plot_Median_Other . Plot_Median_UMIs . Pull_Cluster_Annotation . Pull_Directory_List . QC_Histogram . QC_Plot_GenevsFeature . QC_Plot_UMIvsFeature . QC_Plot_UMIvsGene . QC_Plots_Combined_Vln . QC_Plots_Complexity . QC_Plots_Feature . QC_Plots_Genes . QC_Plots_Mito . QC_Plots_UMIs . Read10X_GEO . Read10X_Multi_Directory . Read10X_h5_GEO . Read10X_h5_Multi_Directory . Read_CellBender_h5_Mat . Read_CellBender_h5_Multi_Directory . Read_CellBender_h5_Multi_File . Read_GEO_Delim . Read_Metrics_10X . Reduction_Loading_Present . Rename_Clusters . Replace_Suffix . Seq_QC_Plot_Alignment_Combined . Seq_QC_Plot_Antisense . Seq_QC_Plot_Basic_Combined . Seq_QC_Plot_Exonic . Seq_QC_Plot_Genes . Seq_QC_Plot_Genome . Seq_QC_Plot_Intergenic . Seq_QC_Plot_Intronic . Seq_QC_Plot_Number_Cells . Seq_QC_Plot_Reads_in_Cells . Seq_QC_Plot_Reads_per_Cell . Seq_QC_Plot_Saturation . Seq_QC_Plot_Total_Genes . Seq_QC_Plot_Transcriptome . Seq_QC_Plot_UMIs . Setup_scRNAseq_Project . Single_Color_Palette . Split_FeatureScatter . Stacked_VlnPlot . Store_Misc_Info_Seurat . Store_Palette_Seurat . Top_Genes_Factor . UnRotate_X . VariableFeaturePlot_scCustom . Variable_Features_ALL_LIGER . VlnPlot_scCustom . ensembl_mito_id . ensembl_ribo_id . ieg_gene_list . msigdb_qc_gene_list . plotFactors_scCustom . scCustomize-package . scCustomize_Palette . theme_ggprism_mod . viridis_shortcut . 
Some associated R codes: Color_Palettes.R . Data.R . Internal_Utilities.R . LIGER_Plotting.R . LIGER_Utilities.R . Nebulosa_Plotting.R . Object_Utilities.R . Plotting_Utilities.R . QC_Plotting_Seq_10X.R . QC_Plotting_Seurat.R . Read_&_Write_Data.R . Seurat_Iterative_Plotting.R . Seurat_Plotting.R . Statistics.R . Statistics_Plotting.R . Utilities.R . zzz.R .  Full scCustomize package functions and examples
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