Package: scCustomize 2.1.2
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:
scCustomize_2.1.2.tar.gz
scCustomize_2.1.2.zip(r-4.5)scCustomize_2.1.2.zip(r-4.4)scCustomize_2.1.2.zip(r-4.3)
scCustomize_2.1.2.tgz(r-4.4-any)scCustomize_2.1.2.tgz(r-4.3-any)
scCustomize_2.1.2.tar.gz(r-4.5-noble)scCustomize_2.1.2.tar.gz(r-4.4-noble)
scCustomize_2.1.2.tgz(r-4.4-emscripten)
scCustomize.pdf |scCustomize.html✨
scCustomize/json (API)
NEWS
# Install 'scCustomize' in R: |
install.packages('scCustomize', repos = c('https://samuel-marsh.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samuel-marsh/sccustomize/issues
- ensembl_mito_id - Ensembl Mito IDs
- ensembl_ribo_id - Ensembl Ribo IDs
- ieg_gene_list - Immediate Early Gene (IEG) gene lists
- msigdb_qc_gene_list - QC Gene Lists
customizationggplot2scrna-seqseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seqvisualization
Last updated 9 months agofrom:fc7a282af3. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 25 2024 |
R-4.5-win | OK | Oct 25 2024 |
R-4.5-linux | OK | Oct 25 2024 |
R-4.4-win | OK | Oct 25 2024 |
R-4.4-mac | OK | Oct 25 2024 |
R-4.3-win | OK | Oct 25 2024 |
R-4.3-mac | OK | Oct 25 2024 |
Exports:Add_Alt_Feature_IDAdd_Cell_ComplexityAdd_Cell_Complexity_LIGERAdd_Cell_Complexity_SeuratAdd_Cell_QC_MetricsAdd_CellBender_DiffAdd_Mito_RiboAdd_Mito_Ribo_LIGERAdd_Mito_Ribo_SeuratAdd_Pct_DiffAdd_Sample_MetaAdd_Top_Gene_Pct_Seuratas.anndataas.LIGERas.SeuratBarcode_PlotBlank_ThemeCase_CheckCell_Highlight_PlotCellBender_Diff_PlotCellBender_Feature_DiffChange_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_scCustomExtract_ModalityExtract_Sample_MetaExtract_Top_MarkersFeature_PresentFeaturePlot_DualAssayFeaturePlot_scCustomFeatureScatter_scCustomFetch_MetaGene_PresentHue_PalIterate_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_FeaturesLiger_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_scCustomPull_Cluster_AnnotationPull_Directory_ListQC_HistogramQC_Plot_GenevsFeatureQC_Plot_UMIvsFeatureQC_Plot_UMIvsGeneQC_Plots_Combined_VlnQC_Plots_ComplexityQC_Plots_FeatureQC_Plots_GenesQC_Plots_MitoQC_Plots_UMIsRead_CellBender_h5_MatRead_CellBender_h5_Multi_DirectoryRead_CellBender_h5_Multi_FileRead_GEO_DelimRead_Metrics_10XRead10X_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_UMIsSetup_scRNAseq_ProjectSingle_Color_PaletteSplit_FeatureScatterSplit_LayersSplit_VectorStacked_VlnPlotStore_Misc_Info_SeuratStore_Palette_Seurattheme_ggprism_modTop_Genes_FactorUnRotate_XUpdated_HGNC_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_scCustom
Dependencies:abindaskpassbase64encbeeswarmBHbitopsbslibcachemCairocaToolscirclizecliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforcatsfsfuturefuture.applygenericsggbeeswarmggplot2ggprismggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjanitorjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestlubridatemagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpaletteerparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprismaticprogressrpromisespurrrR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLrematch2reshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarstudioapiRtsnesassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosnakecasesourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttimechangetinytexutf8uwotvctrsviporviridisLitewithrxfunxtableyamlzoo