Files in eisascience/scCustFx

single-cell custom fxs Package

R/BioStudies_ArrayExpress_based.R R/BulkRNAseq.R R/CellMembrane_based.R R/Colors.R R/DiffusionMap.R R/DotPlotFxs.R R/EnrichmentAnalysis.R R/Excel.R R/Figures_CannedSim.R R/Figures_VL.R R/GO_analysis.R R/GSEA.R R/KEGG_Analysis.R R/LabKey_based.R R/MitoGenes.R R/Monocle.R R/MultiDimScaling.R R/Normalizations.R R/PCA.R R/Pseudotime.R R/SDA_3D.R R/SDA_Seurat.R R/SDA_processing_based.R R/SDA_util.R R/Scale.R R/Seurat_Spatial_based.R R/Seurat_based.R R/Transformations.R R/Umap.R R/Utils.R R/Utils_df.R R/Utils_stats.R R/Utils_tables.R R/Visualizations_Network.R R/Visualizations_PieDonut.R R/Visualizations_Radar.R R/Visualizations_SDA.R R/Visualizations_Seurat_based.R R/Visualizations_general.R R/Visualizations_tables.R R/genes.R R/gg_themes.R R/nih_grant_scraper.R R/old.R R/pipeline_NCBIvsCAT_NHP.R R/scvi.R R/tSNE.R README.md man/BetterViolins.Rd man/BiSplit_DE.Rd man/Bool.CellsGT.Rd man/CalckBET.Rd man/CalculateModuleScoreAvg.Rd man/CellScore_FeaturePlot.Rd man/CellScore_RidgePlot.Rd man/CellScore_VlnPlot.Rd man/Cold2Hot.Rd man/ColorTheme.Rd man/CommonLoadingSDAMat.Rd man/ComputeARI_Ser.Rd man/ComputeLISI_Ser.Rd man/ComputeSilhouette_Ser.Rd man/ComputekBET_ser.Rd man/CreateProteinHeatmap.Rd man/CreateProteinHeatmap.old.Rd man/DesignModelMatrix.Rd man/DotPlot2.Rd man/DownSample_SerObj_perLevel.Rd man/DualFeatGate.Rd man/FeatThrTab_boxplot.Rd man/FeaturePlot_cust.Rd man/FilterSpatial.Rd man/FindAllMarkers_SubsetCoord.Rd man/Find_FOXP3.Rd man/Find_TCR_MAITS.Rd man/GeneOverlapAcrossComps.Rd man/Get.Gene_Info.Rd man/GetAvgExpressionMatrix.Rd man/GetKEGGPathways.Rd man/GetTopKEGG.Rd man/GetTopPathways.Rd man/HeatMap_SDAScore_Thr.Rd man/ImputeSDA2Ser.Rd man/ImputeSDA2SerV2.Rd man/ImputeSDA2SerV3.Rd man/JustDots.Rd man/LoadSCE_ReturnSer.Rd man/LogAdd.Rd man/MDSmyDF.Rd man/Most_Common_Clones.Rd man/Most_Common_Clones_2_Matrix.Rd man/Most_Common_Clones_Per.Rd man/NormalizeAndScaleV2.Rd man/PCAmyDF.Rd man/Perc2Radar.Rd man/PercExprThrTab.Rd man/PercentExpressed.Rd man/PieDonut2.Rd man/PlotDiffComp.Rd man/PlotDiffComp2.Rd man/PlotExprThrTab.Rd man/PlotFeatThrTab.Rd man/PlotHistDensOptima.Rd man/PlotKEGG.Rd man/Plot_Pseudotime_V_Gene.Rd man/Plot_Pseudotime_V_Gene_combo.Rd man/Plot_SDAScoresPerFeature_ser.Rd man/ProduceComboHeatmap.Rd man/ProduceComboHeatmap.old.Rd man/ProduceComboHeatmapFromMatrix.Rd man/PseudoMySeur.Rd man/QuantileADTcounter.Rd man/QuantileEdgeClean.Rd man/Rank_Swarm.Rd man/RearrangeLabelsByFrequency.Rd man/ReduceSerObj_HTO.Rd man/RunComBat.Rd man/RunComBatseq.Rd man/RunHarmony.Rd man/RunKBET.Rd man/RunLiger.Rd man/RunMNN.Rd man/RunScMerge.Rd man/RunScanorama.Rd man/RunSilhouette.Rd man/RunUMAP.Matrix.Rd man/RunUMAP.Matrix.py.Rd man/Run_Integration.Rd man/RuntSNE.Matrix.Rd man/SDA.AddCompStats.Rd man/SDA.GO_Enrichment.Rd man/SDAScoreMeta2Reduction.Rd man/SDA_counts_preproc.Rd man/SDA_ser_preproc.Rd man/SDApostprocessing.Rd man/SDAresChecks.Rd man/STRINGdb_network.Rd man/SaveMy_table.Rd man/Save_LS_Excel.Rd man/Save_LS_ExcelV2.Rd man/Ser2Monocle_MakeNProcess.Rd man/SetDirectionKEGG.Rd man/SingleFeatGate.Rd man/SpatialSer.SlideSeq.local.Rd man/SubsetSerByCoordinates.Rd man/TopGenes_Boxplot.Rd man/TransposeDT.Rd man/UniformSampleDF_FacPor.Rd man/UnsupClust_UMAP_proc.Rd man/VlnPlot_subset.Rd man/WichIn1not2.Rd man/add_quadrant_labels.Rd man/analyzeEnrichment.Rd man/analyzeTable_Enrichment.Rd man/analyze_component_scores.Rd man/autoProcessRawSerObjs.basic.Rd man/autoProcessRawSerObjs.prime.Rd man/avgExpr_norm.Rd man/barplot_vectors.Rd man/cleanmygenes.mouse.Rd man/closest_1_0s.Rd man/colSdColMeans.Rd man/compressSerHD5.Rd man/convert.Human2Mouse.Rd man/convert.Human2Mouse.biomaRt.Rd man/convert.Mouse2Human.biomaRt.Rd man/count_overlap.Rd man/create_gif_LS.Rd man/create_grouped_plot.Rd man/create_qq_plot.Rd man/create_upset_plot.Rd man/discretize_table.Rd man/download_CITEseq.Rd man/download_SeuratHashingCalls.Rd man/draw_volcano_DEseq.Rd man/dropsimNorm.Rd man/dropsimNormV2.Rd man/enrichGOFunction.Rd man/evens.Rd man/find_peaks.Rd man/find_pseudotime.Rd man/frac_to_numeric.Rd man/getFeatWindows.Rd man/getGeneHomology.Rd man/getTopCorrelationPairs.Rd man/get_MitoGeneSet.Rd man/gg_barplot_2waytable.Rd man/gg_barplot_table.Rd man/gg_barplot_table2.Rd man/gg_pie_table.Rd man/gg_tSNE_df.Rd man/go_volcano_plot.Rd man/heatmap_table.Rd man/intersect_perc.Rd man/is.even.Rd man/is.odd.Rd man/is_in_range.Rd man/make_RNA_heatmap.Rd man/make_RNA_heatmap2.Rd man/map_genes.Rd man/normaliseDGEv2.Rd man/normalizeMultipleMatrices.Rd man/odds.Rd man/parse_nih_due_dates.Rd man/parse_single_url.Rd man/plot2Dredux.Rd man/plot3d_seurat.Rd man/plotEnrichment.Rd man/plotEnrichment.old.Rd man/plotGeneExpression.Rd man/plotPCgeneLoadings.Rd man/plot_component_ridge.Rd man/plot_gene_network.Rd man/plot_gsea_volcano.Rd man/plot_heatmap_DEseq.Rd man/plot_knn.Rd man/plot_knn_labels.Rd man/plot_libSize.Rd man/plot_loadings_coordinates.Rd man/plot_loadings_coordinates.seurat.Rd man/plot_loadings_coordinatesV2.Rd man/plot_minium_spanning_tree.Rd man/plot_pca_variance.Rd man/plot_top_fgsea.Rd man/plot_violin_wFeatFilter.Rd man/plot_violin_wpvalue.Rd man/plot_wordcloud.Rd man/predict.SDA.Rd man/prepNormedDGE_SDA.Rd man/princurve_bootstrap.Rd man/process_SCTbase.Rd man/quantile_breaks.Rd man/quantile_norm.Rd man/range01.Rd man/rotate_SDA.Rd man/rotate_df.Rd man/rotate_tsne.Rd man/runSDAv1_2D.Rd man/run_GSEA_from_signature.Rd man/run_bidirectional_enrichment.Rd man/run_bidirectional_fgsea_from_loadings.Rd man/run_fgsea_from_de.Rd man/save_ggplot_list.Rd man/scale_color_gradient_heat1.Rd man/scale_color_gradient_heat2.Rd man/scale_colour_Publication.Rd man/scale_fill_Publication.Rd man/scatter_plot_seurat.Rd man/scrape_arrayexpress.Rd man/screen_components_by_metadata.Rd man/similarity_jaccard_DF.Rd man/similarity_jaccard_LS.Rd man/simulate_3D_data.Rd man/string_overlap.Rd man/summarize_significant_components.Rd man/table2DF.Rd man/theme_Publication.Rd man/theme_simple.Rd man/theme_simple2.Rd man/updateClusterLabels.Rd man/write_nih_deadlines_excel.Rd