API for eisascience/scCustFx
single-cell custom fxs Package
| Global functions | |
|---|---|
| BetterViolins | Man page Source code |
| BiSplit_DE | Man page Source code |
| Bool.CellsGT | Man page Source code |
| CalckBET | Man page Source code |
| CalculateModuleScoreAvg | Man page |
| CellScore_FeaturePlot | Man page Source code |
| CellScore_RidgePlot | Man page Source code |
| CellScore_VlnPlot | Man page Source code |
| Cold2Hot | Man page Source code |
| ColorTheme | Man page Source code |
| CommonLoadingSDAMat | Man page Source code |
| ComputeARI_Ser | Man page Source code |
| ComputeLISI_Ser | Man page Source code |
| ComputeSilhouette_Ser | Man page Source code |
| ComputekBET_ser | Man page Source code |
| CreateProteinHeatmap | Man page Source code |
| CreateProteinHeatmap.old | Man page Source code |
| DesignModelMatrix | Man page |
| DotPlot2 | Man page Source code |
| DownSample_SerObj_perLevel | Man page Source code |
| DualFeatGate | Man page Source code |
| FeatThrTab_boxplot | Man page Source code |
| FeaturePlot_cust | Man page Source code |
| FilterSpatial | Man page Source code |
| FindAllMarkers_SubsetCoord | Man page Source code |
| Find_FOXP3 | Man page Source code |
| Find_TCR_MAITS | Man page Source code |
| GeneOverlapAcrossComps | Man page Source code |
| Get.Gene_Info | Man page Source code |
| GetAvgExpressionMatrix | Man page Source code |
| GetKEGGPathways | Man page Source code |
| GetTopKEGG | Man page Source code |
| GetTopPathways | Man page Source code |
| HeatMap_SDAScore_Thr | Man page Source code |
| ImputeSDA2Ser | Man page Source code |
| ImputeSDA2SerV2 | Man page Source code |
| ImputeSDA2SerV3 | Man page Source code |
| JustDots | Man page Source code |
| LoadSCE_ReturnSer | Man page Source code |
| LogAdd | Man page Source code |
| MDSmyDF | Man page Source code |
| Most_Common_Clones | Man page Source code |
| Most_Common_Clones_2_Matrix | Man page Source code |
| Most_Common_Clones_Per | Man page Source code |
| NormalizeAndScaleV2 | Man page Source code |
| PCAmyDF | Man page |
| Perc2Radar | Man page Source code |
| PercExprThrTab | Man page Source code |
| PercentExpressed | Man page Source code |
| PieDonut2 | Man page Source code |
| PlotDiffComp | Man page Source code |
| PlotDiffComp2 | Man page Source code |
| PlotExprThrTab | Man page Source code |
| PlotFeatThrTab | Man page Source code |
| PlotHistDensOptima | Man page Source code |
| PlotKEGG | Man page Source code |
| Plot_Pseudotime_V_Gene | Man page Source code |
| Plot_Pseudotime_V_Gene_combo | Man page Source code |
| Plot_SDAScoresPerFeature_ser | Man page |
| ProduceComboHeatmap | Man page Source code |
| ProduceComboHeatmap.old | Man page Source code |
| ProduceComboHeatmapFromMatrix | Man page Source code |
| PseudoMySeur | Man page Source code |
| QuantileADTcounter | Man page Source code |
| QuantileEdgeClean | Man page Source code |
| Rank_Swarm | Man page Source code |
| RearrangeLabelsByFrequency | Man page Source code |
| Receptor_Lingand_Sim | Source code |
| ReduceSerObj_HTO | Man page Source code |
| RunComBat | Man page Source code |
| RunComBatseq | Man page Source code |
| RunHarmony | Man page Source code |
| RunKBET | Man page Source code |
| RunLiger | Man page Source code |
| RunMNN | Man page Source code |
| RunScMerge | Man page Source code |
| RunScanorama | Man page Source code |
| RunSilhouette | Man page Source code |
| RunUMAP.Matrix | Man page Source code |
| RunUMAP.Matrix.py | Man page Source code |
| Run_Integration | Man page Source code |
| RuntSNE.Matrix | Man page Source code |
| SDA.AddCompStats | Man page Source code |
| SDA.GO_Enrichment | Man page |
| SDAScoreMeta2Reduction | Man page Source code |
| SDA_counts_preproc | Man page |
| SDA_ser_preproc | Man page Source code |
| SDApostprocessing | Man page Source code |
| SDAresChecks | Man page Source code |
| STRINGdb_network | Man page Source code |
| SaveMy_table | Man page Source code |
| Save_LS_Excel | Man page Source code |
| Save_LS_ExcelV2 | Man page Source code |
| Ser2Monocle_MakeNProcess | Man page Source code |
| SetDirectionKEGG | Man page Source code |
| SingleFeatGate | Man page Source code |
| SpatialSer.SlideSeq.local | Man page Source code |
| SubsetSerByCoordinates | Man page Source code |
| TopGenes_Boxplot | Man page Source code |
| TransposeDT | Man page Source code Source code |
| UniformSampleDF_FacPor | Man page Source code Source code |
| UnsupClust_UMAP_proc | Man page Source code |
| VlnPlot_subset | Man page Source code |
| WichIn1not2 | Man page Source code |
| add_quadrant_labels | Man page Source code |
| analyzeEnrichment | Man page Source code |
| analyzeTable_Enrichment | Man page Source code |
| analyze_component_scores | Man page Source code |
| autoProcessRawSerObjs.basic | Man page Source code |
| autoProcessRawSerObjs.prime | Man page Source code |
| avgExpr_norm | Man page Source code |
| barplot_vectors | Man page Source code |
| cleanmygenes.mouse | Man page Source code |
| closest_1_0s | Man page Source code |
| colSdColMeans | Man page Source code |
| compressSerHD5 | Man page Source code |
| convert.Human2Mouse | Man page Source code |
| convert.Human2Mouse.biomaRt | Man page Source code |
| convert.Mouse2Human.biomaRt | Man page Source code |
| count_overlap | Man page Source code |
| create_gif_LS | Man page Source code |
| create_grouped_plot | Man page Source code |
| create_qq_plot | Man page Source code |
| create_upset_plot | Man page Source code |
| discretize_table | Man page Source code |
| download_CITEseq | Man page |
| download_SeuratHashingCalls | Man page Source code |
| draw_volcano_DEseq | Man page Source code |
| dropsimNorm | Man page Source code |
| dropsimNormV2 | Man page Source code |
| enrichGOFunction | Man page Source code |
| evens | Man page Source code |
| find_peaks | Man page |
| find_pseudotime | Man page Source code |
| frac_to_numeric | Man page Source code |
| getFeatWindows | Man page Source code |
| getGeneHomology | Man page Source code |
| getTopCorrelationPairs | Man page Source code |
| get_MitoGeneSet | Man page Source code |
| gg_barplot_2waytable | Man page Source code |
| gg_barplot_table | Man page Source code |
| gg_barplot_table2 | Man page Source code |
| gg_pie_table | Man page Source code |
| gg_tSNE_df | Man page Source code |
| go_volcano_plot | Man page Source code |
| heatmap_table | Man page Source code |
| intersect_perc | Man page Source code |
| is.even | Man page Source code |
| is.odd | Man page Source code |
| is_in_range | Man page Source code |
| make_RNA_heatmap | Man page Source code |
| make_RNA_heatmap2 | Man page Source code |
| map_genes | Man page Source code |
| normaliseDGEv2 | Man page |
| normalizeMultipleMatrices | Man page Source code |
| odds | Man page Source code |
| parse_nih_due_dates | Man page Source code |
| parse_single_url | Man page Source code |
| plot2Dredux | Man page Source code |
| plot3d_seurat | Man page Source code |
| plotEnrichment | Man page Source code |
| plotEnrichment.old | Man page Source code |
| plotGeneExpression | Man page Source code |
| plotPCgeneLoadings | Man page Source code |
| plot_component_ridge | Man page Source code |
| plot_gene_network | Man page Source code |
| plot_gsea_volcano | Man page Source code |
| plot_heatmap_DEseq | Man page Source code |
| plot_knn | Man page Source code |
| plot_knn_labels | Man page Source code |
| plot_libSize | Man page Source code |
| plot_loadings_coordinates | Man page Source code |
| plot_loadings_coordinates.seurat | Man page Source code |
| plot_loadings_coordinatesV2 | Man page Source code |
| plot_minium_spanning_tree | Man page Source code |
| plot_pca_variance | Man page Source code |
| plot_top_fgsea | Man page Source code |
| plot_violin_wFeatFilter | Man page Source code |
| plot_violin_wpvalue | Man page Source code |
| plot_wordcloud | Man page Source code |
| predict.SDA | Man page Source code |
| prepNormedDGE_SDA | Man page Source code |
| princurve_bootstrap | Man page |
| process_SCTbase | Man page Source code Source code |
| quantile_breaks | Man page Source code |
| quantile_norm | Man page Source code |
| range01 | Man page Source code Source code |
| rotate_SDA | Man page Source code |
| rotate_df | Man page Source code |
| rotate_tsne | Man page Source code |
| runSDAv1_2D | Man page Source code |
| run_GSEA_from_signature | Man page Source code |
| run_bidirectional_enrichment | Man page Source code |
| run_bidirectional_fgsea_from_loadings | Man page Source code |
| run_fgsea_from_de | Man page Source code |
| save_ggplot_list | Man page Source code |
| scale_color_gradient_heat1 | Man page |
| scale_color_gradient_heat2 | Man page |
| scale_colour_Publication | Man page Source code |
| scale_fill_Publication | Man page Source code |
| scatter_plot_seurat | Man page Source code |
| scrape_arrayexpress | Man page Source code |
| screen_components_by_metadata | Man page Source code |
| similarity_jaccard_DF | Man page Source code |
| similarity_jaccard_LS | Man page Source code |
| simulate_3D_data | Man page Source code |
| string_overlap | Man page Source code |
| summarize_significant_components | Man page Source code |
| table2DF | Man page Source code |
| theme_Publication | Man page Source code |
| theme_simple | Man page |
| theme_simple2 | Man page |
| updateClusterLabels | Man page Source code |
| write_nih_deadlines_excel | Man page Source code |
