Man pages for eisascience/scCustFx
single-cell custom fxs Package
| add_quadrant_labels | Add quadrant labels to a ggplot representing a scatterplot |
| analyze_component_scores | Analyze Differences in Component Scores Across Groups |
| analyzeEnrichment | Analyze PC Enrichment |
| analyzeTable_Enrichment | Analyze Enrichment in a Contingency Table |
| autoProcessRawSerObjs.basic | autoProcessRawSerObjs.basic: An automated and basic pipeline... |
| autoProcessRawSerObjs.prime | autoProcessRawSerObjs.prime: An automated and basic pipeline... |
| avgExpr_norm | avgExpr_norm |
| barplot_vectors | barplot vectors side by side |
| BetterViolins | BetterViolins |
| BiSplit_DE | BiSplit_DE |
| Bool.CellsGT | Bool.CellsGT |
| CalckBET | k-Nearest Neighbour Batch Effect Test |
| CalculateModuleScoreAvg | CalculateModuleScoreAvg |
| CellScore_FeaturePlot | Cell Score Feature Plot |
| CellScore_RidgePlot | Cell Score Ridge Plot |
| CellScore_VlnPlot | Cell Score Violin Plot |
| cleanmygenes.mouse | clean gene set of commonly unwanted genes |
| closest_1_0s | Find the closest multiple of 10 to a given number. |
| Cold2Hot | Cold2Hot |
| ColorTheme | ColorTheme |
| colSdColMeans | colSdColMeans |
| CommonLoadingSDAMat | Combine loading matrices across multiple SDA runs |
| compressSerHD5 | compressSerHD5 |
| ComputeARI_Ser | Compute Adjusted Rand Index (ARI) for a Seurat Object |
| ComputekBET_ser | Compute kBET (k-nearest neighbor Batch Effect Test) for a... |
| ComputeLISI_Ser | Compute LISI (Local Inverse Simpson's Index) for a Seurat... |
| ComputeSilhouette_Ser | Compute Silhouette Score for a Seurat Object |
| convert.Human2Mouse | convert.Human2Mouse |
| convert.Human2Mouse.biomaRt | convert.Human2Mouse.biomaRt |
| convert.Mouse2Human.biomaRt | convert.Mouse2Human.biomaRt |
| count_overlap | Counts the overlap of items in rows per column feature |
| create_gif_LS | Make a GIF from plot list |
| create_grouped_plot | Create a grouped plot with percentage labels in the legend. |
| CreateProteinHeatmap | Create a protein heatmap |
| CreateProteinHeatmap.old | Create a protein heatmap old ver |
| create_qq_plot | Create a QQ Plot |
| create_upset_plot | Create an UpSet plot from a list of sets |
| DesignModelMatrix | Create a Model Matrix for Experimental Design |
| discretize_table | discretize_table |
| DotPlot2 | Enhanced Dot Plot Visualization for Seurat Objects |
| download_CITEseq | download_CITEseq |
| download_SeuratHashingCalls | download_SeuratHashingCalls |
| DownSample_SerObj_perLevel | DownSample_SerObj_perLevel |
| draw_volcano_DEseq | Draw a volcano plot for one contrast derived from DEseq |
| dropsimNorm | dropsimNorm |
| dropsimNormV2 | dropsimNormV2 speeds up using sparse matrix fx as much as... |
| DualFeatGate | Perform dual-feature gating on a Seurat object |
| enrichGOFunction | Perform GO Enrichment Analysis and Visualization |
| evens | evens |
| FeatThrTab_boxplot | Generate a boxplot with jittered points for the percentage of... |
| FeaturePlot_cust | Generate a FeaturePlot_cust which is a scatter plot with gene... |
| FilterSpatial | Filter Spatial data and plot before and after cell loss |
| FindAllMarkers_SubsetCoord | Subset a Seurat object by coordinates and find DE genes |
| Find_FOXP3 | Find_FOXP3 Identify FOXP3+ cells |
| find_peaks | find_peaks |
| find_pseudotime | Find Pseudotime |
| Find_TCR_MAITS | Find_TCR_MAITS Identify TRAV1-2 cells and Classical MAITS as... |
| frac_to_numeric | frac_to_numeric |
| GeneOverlapAcrossComps | Gene overlap across components |
| GetAvgExpressionMatrix | Calculate Average Expression Matrix for Marker Genes in... |
| getFeatWindows | Get feature windows |
| getGeneHomology | Retrieve Homology Information from Ensembl |
| Get.Gene_Info | Get.Gene_Info |
| GetKEGGPathways | GetKEGGPathways |
| get_MitoGeneSet | get_MitoGeneSet |
| getTopCorrelationPairs | Get Top Correlation Pairs from a Correlation Matrix |
| GetTopKEGG | GetTopKEGG |
| GetTopPathways | GetTopPathways |
| gg_barplot_2waytable | gg_barplot_2waytable, aka OOSAP::PlotMyTable |
| gg_barplot_table | gg_barplot_table |
| gg_barplot_table2 | gg_barplot_table2 |
| gg_pie_table | gg_pie_table |
| gg_tSNE_df | gg_tSNE_df |
| go_volcano_plot | GO Volcano Plot |
| HeatMap_SDAScore_Thr | This function generates a Heatmap of thresholding SDA score |
| heatmap_table | heatmap_table |
| ImputeSDA2Ser | This function to add imputed scores from gene loading |
| ImputeSDA2SerV2 | This function to add imputed scores from gene loading |
| ImputeSDA2SerV3 | This function to add imputed scores from gene loading, V3 is... |
| intersect_perc | Compute the percentage of intersection between two character... |
| is.even | is.even |
| is_in_range | Check if a value falls within a distribution range defined by... |
| is.odd | is.odd |
| JustDots | Custom Dot Plot Visualization for Seurat Objects |
| LoadSCE_ReturnSer | load a h5ad SCE object and convert to seurat |
| LogAdd | LogAdd |
| make_RNA_heatmap | Make an RNA heatmap |
| make_RNA_heatmap2 | Plot RNA heatmap v2, no re-normalization of the data |
| map_genes | Map Gene Identifiers in DESeq2 Results |
| MDSmyDF | MDS Plot of Data Frame |
| Most_Common_Clones | Most_Common_Clones Function to compute the most common clones... |
| Most_Common_Clones_2_Matrix | Most_Common_Clones_2_Matrix A function that takes in a list,... |
| Most_Common_Clones_Per | Most_Common_Clones_Per Function to compute the most common... |
| normaliseDGEv2 | normaliseDGEv2 |
| NormalizeAndScaleV2 | NormalizeAndScaleV2 a customized version from CellMembrane |
| normalizeMultipleMatrices | Normalize multiple matrices using quantile normalization |
| odds | odds |
| parse_nih_due_dates | Parse Multiple NIH Grant Pages and Combine Key Dates Data |
| parse_single_url | Parse a NIH Grant Page for Key Dates and Metadata |
| PCAmyDF | Principal Component Analysis (PCA) Plot |
| Perc2Radar | Perc2Radar |
| PercentExpressed | Calculate the percent expressed cells for each group in a... |
| PercExprThrTab | PercExprThrTab |
| PieDonut2 | Plot a pie and donut chart |
| plot2Dredux | Plot 2D Dimensionality Reduction |
| plot3d_seurat | Plot 3D visualization of Seurat object |
| plot_component_ridge | Generate Ridge Plot of Component Scores by Metadata Feature |
| PlotDiffComp | Plots destiny's Diffusion Map |
| PlotDiffComp2 | Plots destiny's Diffusion Map. This function includes... |
| plotEnrichment | Plot Enrichment |
| plotEnrichment.old | Plot Enrichment |
| PlotExprThrTab | PlotExprThrTab |
| PlotFeatThrTab | PlotFeatThrTab |
| plotGeneExpression | Plot Gene Expression in Seurat Object |
| plot_gene_network | Make a GIF from plot list |
| plot_gsea_volcano | Volcano Plot for GSEA Results with Improved Labeling |
| plot_heatmap_DEseq | Plot a heatmap of differentially expressed genes for a single... |
| PlotHistDensOptima | PlotHistDensOptima |
| PlotKEGG | PlotKEGG |
| plot_knn | Plot k-Nearest Neighbors Graph |
| plot_knn_labels | Plot k-Nearest Neighbors Graph with multiple lables |
| plot_libSize | plot_libSize |
| plot_loadings_coordinates | This function generates a plot of gene loadings along genomic... |
| plot_loadings_coordinates.seurat | This function generates a plot of gene loadings along genomic... |
| plot_loadings_coordinatesV2 | Plot Loadings Coordinates with Genomic Information |
| plot_minium_spanning_tree | Plot Minimum Spanning Tree |
| plot_pca_variance | Plot Explained Variance of Principal Components |
| plotPCgeneLoadings | scatter-bubble style of selected PCs and genes |
| Plot_Pseudotime_V_Gene | Plot a scatter plot with smoothed lines for selected features |
| Plot_Pseudotime_V_Gene_combo | Plot Violin Plots of Gene Expression by Group combo version |
| Plot_SDAScoresPerFeature_ser | Plot a heatmap of tabulation of SDA score vs meta |
| plot_top_fgsea | Plot Top Enriched Pathways from fgsea Results |
| plot_violin_wFeatFilter | Plot Violin Plots of Gene Expression by Group |
| plot_violin_wpvalue | Plot violin plots with Wilcoxon p-values |
| plot_wordcloud | Plot a word cloud from a named vector of word counts |
| predict.SDA | Predict using SDA |
| prepNormedDGE_SDA | Prepare and Save Normalized Gene Expression Data for SDA |
| princurve_bootstrap | Principal Curve Bootstrap |
| process_SCTbase | process Seurat Spatial object via SCT |
| ProduceComboHeatmap | Produce a combination heatmap |
| ProduceComboHeatmapFromMatrix | Produce Combo Heatmap From Matrix |
| ProduceComboHeatmap.old | Produce a combination heatmap old ver |
| PseudoMySeur | PseudoMySeur |
| QuantileADTcounter | QuantileADTcounter |
| quantile_breaks | Quantile Breaks |
| QuantileEdgeClean | QuantileEdgeClean |
| quantile_norm | quantile_norm |
| range01 | Convert Vector to 0-1 Range |
| Rank_Swarm | Rank a feature and plot a swarm grouped by select categorical... |
| RearrangeLabelsByFrequency | RearrangeLabelsByFrequency |
| ReduceSerObj_HTO | ReduceSerObj_HTO |
| rotate_df | rotate_df |
| rotate_SDA | Rotate SDA factorisation |
| rotate_tsne | rotate_tsne |
| run_bidirectional_enrichment | Run Gene Set Enrichment Analysis on Loadings |
| run_bidirectional_fgsea_from_loadings | Run Bidirectional fgsea Analysis from Gene Loadings |
| RunComBat | RunComBat |
| RunComBatseq | RunComBatseq |
| run_fgsea_from_de | Run GSEA Using fgsea |
| run_GSEA_from_signature | Run GSEA from a DE Results Data Frame and a Gene Signature |
| RunHarmony | RunHarmony |
| Run_Integration | Run Integration Pipeline for Single-Cell Data |
| RunKBET | RunKBET |
| RunLiger | RunLiger |
| RunMNN | RunMNN |
| RunScanorama | RunScanorama |
| RunScMerge | RunScMerge |
| runSDAv1_2D | Run SDA V1.1 in 2D i.e., matrix form |
| RunSilhouette | RunSilhouette |
| RuntSNE.Matrix | This function to run tsne on matrix |
| RunUMAP.Matrix | Perform UMAP Dimensionality Reduction on a Matrix |
| RunUMAP.Matrix.py | Run UMAP dimensionality reduction on a matrix using... |
| save_ggplot_list | Save a patchwork of ggplot figures to a file |
| Save_LS_Excel | Save a List of DE Results to an Excel File |
| Save_LS_ExcelV2 | Save DE Results to Excel, Splitting by Up/Down Regulation |
| SaveMy_table | Generate and Save/Display a Styled Table |
| scale_color_gradient_heat1 | scale_color_gradient_heat1 |
| scale_color_gradient_heat2 | scale_color_gradient_heat2 |
| scale_colour_Publication | Scale Colour Publication |
| scale_fill_Publication | Scale Fill Publication |
| scatter_plot_seurat | scatter_plot_seurat |
| scrape_arrayexpress | Scrape ArrayExpress metadata and fastq.gz links |
| screen_components_by_metadata | Screen All Components for Differences by Metadata Feature |
| SDA.AddCompStats | SDA.AddCompStats |
| SDA_counts_preproc | Preprocess Raw Count Matrix for SDA |
| SDA.GO_Enrichment | Perform Gene Ontology Enrichment Analysis on SDA Components |
| SDApostprocessing | Post-process Single-cell Data Analysis (SDA) Results |
| SDAresChecks | Diagnostic Checks on SDA Results |
| SDAScoreMeta2Reduction | Create a new dimension reduction object using SDA scores |
| SDA_ser_preproc | Preprocess Seurat Object for Single-cell Data Analysis |
| Ser2Monocle_MakeNProcess | Ser2Monocle_MakeNProcess |
| SetDirectionKEGG | SetDirectionKEGG |
| similarity_jaccard_DF | similarity overlap dataframe |
| similarity_jaccard_LS | similarity_overlap list |
| simulate_3D_data | Simulate 3D Data |
| SingleFeatGate | Perform dual-feature gating on a Seurat object |
| SpatialSer.SlideSeq.local | Create a Seurat object from Spatial SlideSeq data |
| STRINGdb_network | STRING Network from Gene List |
| string_overlap | Calculate gene overlap between two data frames |
| SubsetSerByCoordinates | SubsetSerByCoordinates |
| summarize_significant_components | Summarize Significant Components Across Metadata Features |
| table2DF | Covert a table to a dataframe |
| theme_Publication | Theme Publication |
| theme_simple | theme_simple remove legend, and axis text |
| theme_simple2 | theme_simple remove legend, axis, and title with base size 20 |
| TopGenes_Boxplot | Plot Top Expressed Genes |
| TransposeDT | transposedt |
| UniformSampleDF_FacPor | UniformSampleDF_FacPor |
| UnsupClust_UMAP_proc | Perform unsupervised clustering and UMAP reduction |
| updateClusterLabels | Update Cluster Labels Based on Frequency |
| VlnPlot_subset | Calculate the percent expressed cells for each group in a... |
| WichIn1not2 | WichIn1not2 |
| write_nih_deadlines_excel | Write NIH Deadline Data to Excel |
