Package: scCustomize 3.0.1

Samuel Marsh

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

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.

Authors:Samuel Marsh [aut, cre], Ming Tang [ctb], Velina Kozareva [ctb], Lucas Graybuck [ctb]

scCustomize_3.0.1.tar.gz
scCustomize_3.0.1.tar.gz(r-4.5-noble)scCustomize_3.0.1.tar.gz(r-4.4-noble)
scCustomize_3.0.1.tgz(r-4.4-emscripten)
scCustomize.pdf |scCustomize.html✨
scCustomize/json (API)
NEWS

# Install 'scCustomize' in R:
install.packages('scCustomize', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/samuel-marsh/sccustomize/issues

Pkgdown site:https://samuel-marsh.github.io

Datasets:

4.89 score 1.1k scripts 3.5k downloads 167 exports 168 dependencies

Last updated 8 days agofrom:ded1a2109e. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-linuxOKDec 18 2024

Exports:Add_Alt_Feature_IDAdd_Cell_ComplexityAdd_Cell_Complexity_LIGERAdd_Cell_Complexity_SeuratAdd_Cell_QC_MetricsAdd_CellBender_DiffAdd_HemoAdd_Mito_RiboAdd_Mito_Ribo_LIGERAdd_Mito_Ribo_SeuratAdd_Pct_DiffAdd_Sample_MetaAdd_Top_Gene_PctAdd_Top_Gene_Pct_Seuratas.anndataas.LIGERas.SeuratBarcode_PlotBlank_ThemeCase_CheckCell_Highlight_PlotCellBender_Diff_PlotCellBender_Feature_DiffCellsCells_by_Identities_LIGERCells_per_SampleChange_Delim_AllChange_Delim_PrefixChange_Delim_SuffixCheckMatrix_scCustomCluster_Highlight_PlotCluster_Stats_All_SamplesClustered_DotPlotColorBlind_PalConvert_AssayCopy_From_GCPCopy_To_GCPCreate_10X_H5Create_CellBender_Merged_SeuratCreate_Cluster_Annotation_FileDark2_PalDimPlot_All_SamplesDimPlot_LIGERDimPlot_scCustomDiscretePalette_scCustomizeDotPlot_scCustomEmbeddingsExtract_ModalityExtract_Sample_MetaExtract_Top_MarkersFactor_Cor_PlotFeature_PresentFeaturePlot_DualAssayFeaturePlot_scCustomFeaturesFeatureScatter_scCustomFetch_MetaFind_Factor_CorGene_PresentHue_PalIdentsIdents<-Iterate_Barcode_Rank_PlotIterate_Cluster_Highlight_PlotIterate_DimPlot_bySampleIterate_FeaturePlot_scCustomIterate_Meta_Highlight_PlotIterate_PC_Loading_PlotsIterate_Plot_Density_CustomIterate_Plot_Density_JointIterate_VlnPlot_scCustomJCO_FourLiger_to_SeuratMAD_StatsMedian_StatsMerge_Seurat_ListMerge_Sparse_Data_AllMerge_Sparse_Multimodal_AllMeta_Highlight_PlotMeta_NumericMeta_PresentMeta_Present_LIGERMeta_Remove_SeuratMove_LegendNavyAndOrangePalettePlotPC_PlottingPercent_ExpressingPlot_Cells_per_SamplePlot_Density_CustomPlot_Density_Joint_OnlyPlot_Median_GenesPlot_Median_MitoPlot_Median_OtherPlot_Median_UMIsplotFactors_scCustomProportion_PlotPull_Cluster_AnnotationPull_Directory_ListQC_HistogramQC_Plot_GenevsFeatureQC_Plot_UMIvsFeatureQC_Plot_UMIvsGeneQC_Plots_Combined_VlnQC_Plots_ComplexityQC_Plots_FeatureQC_Plots_GenesQC_Plots_MitoQC_Plots_UMIsRandom_Cells_DownsampleRead_CellBender_h5_MatRead_CellBender_h5_Multi_DirectoryRead_CellBender_h5_Multi_FileRead_GEO_DelimRead_Metrics_10XRead_Metrics_CellBenderRead10X_GEORead10X_h5_GEORead10X_h5_Multi_DirectoryRead10X_Multi_DirectoryReduction_Loading_PresentRename_ClustersReplace_SuffixscCustomize_PaletteSeq_QC_Plot_Alignment_CombinedSeq_QC_Plot_AntisenseSeq_QC_Plot_Basic_CombinedSeq_QC_Plot_ExonicSeq_QC_Plot_GenesSeq_QC_Plot_GenomeSeq_QC_Plot_IntergenicSeq_QC_Plot_IntronicSeq_QC_Plot_Number_CellsSeq_QC_Plot_Reads_in_CellsSeq_QC_Plot_Reads_per_CellSeq_QC_Plot_SaturationSeq_QC_Plot_Total_GenesSeq_QC_Plot_TranscriptomeSeq_QC_Plot_UMIsseq_zerosSetup_scRNAseq_ProjectSingle_Color_PaletteSpatialDimPlot_scCustomSplit_FeatureScatterSplit_LayersSplit_VectorStacked_VlnPlotStore_Misc_Info_SeuratStore_Palette_SeuratSubset_LIGERtheme_ggprism_modTop_Genes_FactorUnRotate_XUpdated_HGNC_SymbolsUpdated_MGI_SymbolsVariable_Features_ALL_LIGERVariableFeaturePlot_scCustomviridis_dark_highviridis_inferno_dark_highviridis_inferno_light_highviridis_light_highviridis_magma_dark_highviridis_magma_light_highviridis_plasma_dark_highviridis_plasma_light_highVlnPlot_scCustomWhichCells

Dependencies:abindaskpassbase64encbeeswarmBHbitopsbslibcachemCairocaToolscirclizecliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforcatsfsfuturefuture.applygenericsggbeeswarmggplot2ggprismggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjanitorjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestlubridatemagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpaletteerparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprismaticprogressrpromisespurrrR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLrematch2reshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarstudioapiRtsnesassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosnakecasesourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttimechangetinytexutf8uwotvctrsviporviridisLitewithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Add Alternative Feature IDsAdd_Alt_Feature_ID
Add Cell ComplexityAdd_Cell_Complexity Add_Cell_Complexity.liger Add_Cell_Complexity.Seurat
Add Multiple Cell Quality Control Values with Single FunctionAdd_Cell_QC_Metrics Add_Cell_QC_Metrics.liger Add_Cell_QC_Metrics.Seurat
Calculate and add differences post-cell bender analysisAdd_CellBender_Diff
Add Hemoglobin percentagesAdd_Hemo Add_Hemo.liger Add_Hemo.Seurat
Add Mito and Ribo percentagesAdd_Mito_Ribo Add_Mito_Ribo.liger Add_Mito_Ribo.Seurat
Add percentage difference to DE resultsAdd_Pct_Diff
Add Sample Level Meta DataAdd_Sample_Meta
Add Percent of High Abundance GenesAdd_Top_Gene_Pct Add_Top_Gene_Pct.liger Add_Top_Gene_Pct.Seurat
Convert objects to anndata objectsas.anndata as.anndata.liger as.anndata.Seurat
Convert objects to LIGER objectsas.LIGER as.LIGER.list as.LIGER.Seurat
Convert objects to 'Seurat' objectsas.Seurat.liger
Create Barcode Rank PlotBarcode_Plot
Blank ThemeBlank_Theme
Check for alternate case featuresCase_Check
Meta Highlight PlotCell_Highlight_Plot
Plot Number of Cells/Nuclei per SampleCellBender_Diff_Plot
CellBender Feature DifferencesCellBender_Feature_Diff
Extract Cells by identityCells_by_Identities_LIGER
Cells per SampleCells_per_Sample
Extract Cells from LIGER ObjectCells.liger
Change all delimiters in cell nameChange_Delim_All
Change barcode prefix delimiterChange_Delim_Prefix
Change barcode suffix delimiterChange_Delim_Suffix
Check Matrix ValidityCheckMatrix_scCustom
Cluster Highlight PlotCluster_Highlight_Plot
Calculate Cluster StatsCluster_Stats_All_Samples
Clustered DotPlotClustered_DotPlot
Color Universal Design Short PaletteColorBlind_Pal
Convert between Seurat Assay typesConvert_Assay
Copy folder from GCP bucket from R ConsoleCopy_From_GCP
Copy folder to GCP bucket from R ConsoleCopy_To_GCP
Create H5 from 10X OutputsCreate_10X_H5
Create Seurat Object with Cell Bender and Raw dataCreate_CellBender_Merged_Seurat
Create cluster annotation csv fileCreate_Cluster_Annotation_File
Dark2 PaletteDark2_Pal
DimPlot by Meta Data ColumnDimPlot_All_Samples
DimPlot LIGER VersionDimPlot_LIGER
DimPlot with modified default settingsDimPlot_scCustom
Discrete color palettesDiscretePalette_scCustomize
Customized DotPlotDotPlot_scCustom
Extract matrix of embeddingsEmbeddings.liger
Ensembl Hemo IDsensembl_hemo_id
Immediate Early Gene (IEG) gene listsensembl_ieg_list
Ensembl Mito IDsensembl_mito_id
Ensembl Ribo IDsensembl_ribo_id
Extract multi-modal data into list by modalityExtract_Modality
Extract sample level meta.dataExtract_Sample_Meta
Extract Top N Marker GenesExtract_Top_Markers
Factor Correlation PlotFactor_Cor_Plot
Check if genes/features are presentFeature_Present
Customize FeaturePlot of two assaysFeaturePlot_DualAssay
Customize FeaturePlotFeaturePlot_scCustom
Extract Features from LIGER ObjectFeatures.liger
Modified version of FeatureScatterFeatureScatter_scCustom
Get meta data from objectFetch_Meta Fetch_Meta.liger Fetch_Meta.Seurat
Find Factor CorrelationsFind_Factor_Cor
Hue_PalHue_Pal
Extract or set default identities from objectIdents.liger Idents<-.liger
Immediate Early Gene (IEG) gene listsieg_gene_list
Iterative Barcode Rank PlotsIterate_Barcode_Rank_Plot
Iterate Cluster Highlight PlotIterate_Cluster_Highlight_Plot
Iterate DimPlot By SampleIterate_DimPlot_bySample
Iterative Plotting of Gene Lists using Custom FeaturePlotsIterate_FeaturePlot_scCustom
Iterate Meta Highlight PlotIterate_Meta_Highlight_Plot
Iterate PC Loading PlotsIterate_PC_Loading_Plots
Iterative Plotting of Gene Lists using Custom Density PlotsIterate_Plot_Density_Custom
Iterative Plotting of Gene Lists using Custom Joint Density PlotsIterate_Plot_Density_Joint
Iterative Plotting of Gene Lists using VlnPlot_scCustomIterate_VlnPlot_scCustom
Four Color Palette (JCO)JCO_Four
Create a Seurat object containing the data from a liger object *[Soft-deprecated]*Liger_to_Seurat
Median Absolute Deviation StatisticsMAD_Stats
Median StatisticsMedian_Stats
Merge a list of Seurat ObjectsMerge_Seurat_List
Merge a list of Sparse MatricesMerge_Sparse_Data_All
Merge a list of Sparse Matrices contain multi-modal data.Merge_Sparse_Multimodal_All
Meta Highlight PlotMeta_Highlight_Plot
Check if meta data columns are numericMeta_Numeric
Check if meta data are presentMeta_Present
Remove meta data columns containing Seurat DefaultsMeta_Remove_Seurat
Move Legend PositionMove_Legend
QC Gene Listsmsigdb_qc_ensembl_list
QC Gene Listsmsigdb_qc_gene_list
Navy and Orange Dual Color PaletteNavyAndOrange
Plot color palette in viewerPalettePlot
PC PlotsPC_Plotting
Calculate percent of expressing cellsPercent_Expressing
Plot Number of Cells/Nuclei per SamplePlot_Cells_per_Sample
Nebulosa Density PlotPlot_Density_Custom
Nebulosa Joint Density PlotPlot_Density_Joint_Only
Plot Median Genes per Cell per SamplePlot_Median_Genes
Plot Median Percent Mito per Cell per SamplePlot_Median_Mito
Plot Median other variable per Cell per SamplePlot_Median_Other
Plot Median UMIs per Cell per SamplePlot_Median_UMIs
Customized version of plotFactorsplotFactors_scCustom
Cell Proportion PlotProportion_Plot
Pull cluster information from annotation csv file.Pull_Cluster_Annotation
Pull Directory ListPull_Directory_List
QC Histogram PlotsQC_Histogram
QC Plots Genes vs MiscQC_Plot_GenevsFeature
QC Plots UMI vs MiscQC_Plot_UMIvsFeature
QC Plots Genes vs UMIsQC_Plot_UMIvsGene
QC Plots Genes, UMIs, & % MitoQC_Plots_Combined_Vln
QC Plots Cell "Complexity"QC_Plots_Complexity
QC Plots FeatureQC_Plots_Feature
QC Plots GenesQC_Plots_Genes
QC Plots MitoQC_Plots_Mito
QC Plots UMIsQC_Plots_UMIs
Randomly downsample by identityRandom_Cells_Downsample
Load CellBender h5 matrices (corrected)Read_CellBender_h5_Mat
Load CellBender h5 matrices (corrected) from multiple directoriesRead_CellBender_h5_Multi_Directory
Load CellBender h5 matrices (corrected) from multiple filesRead_CellBender_h5_Multi_File
Load in NCBI GEO data formatted as single file per sampleRead_GEO_Delim
Read Overall Statistics from 10X Cell Ranger CountRead_Metrics_10X
Read Overall Statistics from CellBenderRead_Metrics_CellBender
Load in NCBI GEO data from 10XRead10X_GEO
Load in NCBI GEO data from 10X in HDF5 file formatRead10X_h5_GEO
Load 10X h5 count matrices from multiple directoriesRead10X_h5_Multi_Directory
Load 10X count matrices from multiple directoriesRead10X_Multi_Directory
Check if reduction loadings are presentReduction_Loading_Present
Rename ClustersRename_Clusters Rename_Clusters.liger Rename_Clusters.Seurat
Replace barcode suffixesReplace_Suffix
Color Palette Selection for scCustomizescCustomize_Palette
QC Plots Sequencing metrics (Alignment) (Layout)Seq_QC_Plot_Alignment_Combined
QC Plots Sequencing metrics (Alignment)Seq_QC_Plot_Antisense
QC Plots Sequencing metrics (Layout)Seq_QC_Plot_Basic_Combined
QC Plots Sequencing metrics (Alignment)Seq_QC_Plot_Exonic
QC Plots Sequencing metricsSeq_QC_Plot_Genes
QC Plots Sequencing metrics (Alignment)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 metricsSeq_QC_Plot_Number_Cells
QC Plots Sequencing metricsSeq_QC_Plot_Reads_in_Cells
QC Plots Sequencing metricsSeq_QC_Plot_Reads_per_Cell
QC Plots Sequencing metricsSeq_QC_Plot_Saturation
QC Plots Sequencing metricsSeq_QC_Plot_Total_Genes
QC Plots Sequencing metrics (Alignment)Seq_QC_Plot_Transcriptome
QC Plots Sequencing metricsSeq_QC_Plot_UMIs
Create sequence with zerosseq_zeros
Setup project directory structureSetup_scRNAseq_Project
Single Color Palettes for PlottingSingle_Color_Palette
SpatialDimPlot with modified default settingsSpatialDimPlot_scCustom
Split Seurat object into layersSplit_Layers
Split vector into listSplit_Vector
Stacked Violin PlotStacked_VlnPlot
Store misc data in Seurat objectStore_Misc_Info_Seurat
Store color palette in Seurat objectStore_Palette_Seurat
Subset LIGER objectSubset_LIGER
Modified ggprism themetheme_ggprism_mod
Extract top loading genes for LIGER factorTop_Genes_Factor
Unrotate x axis on VlnPlotUnRotate_X
Update HGNC Gene SymbolsUpdated_HGNC_Symbols
Update MGI Gene SymbolsUpdated_MGI_Symbols
Perform variable gene selection over whole datasetVariable_Features_ALL_LIGER
Custom Labeled Variable Features PlotVariableFeaturePlot_scCustom
Viridis Shortcutsviridis_dark_high viridis_inferno_dark_high viridis_inferno_light_high viridis_light_high viridis_magma_dark_high viridis_magma_light_high viridis_plasma_dark_high viridis_plasma_light_high
VlnPlot with modified default settingsVlnPlot_scCustom
Extract Cells for particular identityWhichCells.liger