Man pages for bulkAnalyseR
Interactive Shiny App for Bulk Sequencing Data
| calculate_condition_mean_sd_per_gene | Calculate statistics for each gene of an expression matrix... |
| crossPanel | Generate the cross plot panel of the shiny app |
| cross_plot | Create a cross plot comparing differential expression (DE)... |
| DEanalysis | Perform differential expression (DE) analysis on an... |
| DEpanel | Generate the DE panel of the shiny app |
| DEplotPanel | Generate the DE plot plot panel of the shiny app |
| DEsummaryPanel | Generate the DE summary panel of the shiny app |
| determine_uds | Determine the pattern between two intervals |
| enrichmentPanel | Generate the enrichment panel of the shiny app |
| expression_heatmap | Create heatmap of an expression matrix |
| find_regulators_with_recurring_edges | Find recurring regulators |
| generateShinyApp | Generate all files required for an autonomous shiny app |
| genes_barplot | Create a bar plot of expression for selected genes across... |
| get_link_list_rename | Convert the adjacency matrix to network links |
| GRNCisPanel | Generate the GRN cis integration panel of the shiny app |
| GRNCustomPanel | Generate the GRN custom integration panel of the shiny app |
| GRNpanel | Generate the GRN panel of the shiny app |
| GRNTransPanel | Generate the GRN trans integration panel of the shiny app |
| infer_GRN | Perform GRN inference |
| jaccard_heatmap | Create a heatmap of the Jaccard similarity index (JSI)... |
| jaccard_index | Calculate the Jaccard similarity index (JSI) between two... |
| landingPanel | Generate the landing page panel of the shiny app |
| make_heatmap_matrix | Create a matrix of the average expression of each gene in... |
| make_pattern_matrix | Create a matrix of the patterns between conditions |
| ma_plot | Create an MA plot visualising differential expression (DE)... |
| modalityPanel | Generate an app panel for a modality |
| noisyr_counts_with_plot | Apply a modified noisyR counts pipeline printing a plot |
| patternPanel | Generate the expression patterns panel of the shiny app |
| pipe | Pipe operator |
| plot_GRN | Plot a GRN |
| plot_line_pattern | Create a line plot of average expression across conditions |
| plot_pca | Create a principal component analysis (PCA) plot the samples... |
| plot_upset | Visualise the overlap of edges between different networks |
| preprocessExpressionMatrix | Pre-process the expression matrix before generating the shiny... |
| preprocess_miRTarBase | Creates a comparison table for miRTarBase to be used for... |
| qc_density_plot | Create a density plot of log2 expression across samples of an... |
| QCpanel | Generate the QC panel of the shiny app |
| qc_violin_plot | Create a violin/box plot of expression across samples of an... |
| rescale_matrix | Rescale a matrix |
| sampleSelectPanel | Generate the sample select panel of the shiny app |
| scatter_plot | Create a scatter plot of expression between two samples of an... |
| volcano_plot | Create a volcano plot visualising differential expression... |
