Interactive Shiny App for Bulk Sequencing Data


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Documentation for package ‘bulkAnalyseR’ version 1.0.0

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calculate_condition_mean_sd_per_gene Calculate statistics for each gene of an expression matrix given a grouping
crossPanel Generate the cross plot panel of the shiny app
crossPanelServer Generate the cross plot panel of the shiny app
crossPanelUI Generate the cross plot panel of the shiny app
cross_plot Create a cross plot comparing differential expression (DE) results
DEanalysis Perform differential expression (DE) analysis on an expression matrix
DEanalysis_deseq2 Perform differential expression (DE) analysis on an expression matrix
DEanalysis_edger Perform differential expression (DE) analysis on an expression matrix
DEpanel Generate the DE panel of the shiny app
DEpanelServer Generate the DE panel of the shiny app
DEpanelUI Generate the DE panel of the shiny app
DEplotPanel Generate the DE plot plot panel of the shiny app
DEplotPanelServer Generate the DE plot plot panel of the shiny app
DEplotPanelUI Generate the DE plot plot panel of the shiny app
DEsummaryPanel Generate the DE summary panel of the shiny app
DEsummaryPanelServer Generate the DE summary panel of the shiny app
DEsummaryPanelUI 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
enrichmentPanelServer Generate the enrichment panel of the shiny app
enrichmentPanelUI 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
get_link_list_rename Convert the adjacency matrix to network links
GRNCisPanel Generate the GRN cis integration panel of the shiny app
GRNCisPanelServer Generate the GRN cis integration panel of the shiny app
GRNCisPanelUI Generate the GRN cis integration panel of the shiny app
GRNCustomPanel Generate the GRN custom integration panel of the shiny app
GRNCustomPanelServer Generate the GRN custom integration panel of the shiny app
GRNCustomPanelUI Generate the GRN custom integration panel of the shiny app
GRNpanel Generate the GRN panel of the shiny app
GRNpanelServer Generate the GRN panel of the shiny app
GRNpanelUI Generate the GRN panel of the shiny app
GRNTransPanel Generate the GRN trans integration panel of the shiny app
GRNTransPanelServer Generate the GRN trans integration panel of the shiny app
GRNTransPanelUI 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) between samples of an experiment
jaccard_index Calculate the Jaccard similarity index (JSI) between two vectors
landingPanel Generate the landing page panel of the shiny app
landingPanelServer Generate the landing page panel of the shiny app
landingPanelUI Generate the landing page panel of the shiny app
make_heatmap_matrix Create a matrix of the average expression of each gene in each condition
make_pattern_matrix Create a matrix of the patterns between conditions
ma_enhance Create an MA plot visualising differential expression (DE) results
ma_plot Create an MA plot visualising differential expression (DE) results
modalityPanel Generate an app panel for a modality
modalityPanelServer Generate an app panel for a modality
modalityPanelUI 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
patternPanelServer Generate the expression patterns panel of the shiny app
patternPanelUI Generate the expression patterns panel of the shiny app
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 of an experiment
plot_upset Visualise the overlap of edges between different networks
preprocessExpressionMatrix Pre-process the expression matrix before generating the shiny app
preprocess_miRTarBase Creates a comparison table for miRTarBase to be used for custom integration
QCpanel Generate the QC panel of the shiny app
QCpanelServer Generate the QC panel of the shiny app
QCpanelUI Generate the QC panel of the shiny app
rescale_matrix Rescale a matrix
sampleSelectPanel Generate the sample select panel of the shiny app
sampleSelectPanelServer Generate the sample select panel of the shiny app
sampleSelectPanelUI Generate the sample select panel of the shiny app
volcano_enhance Create a volcano plot visualising differential expression (DE) results
volcano_plot Create a volcano plot visualising differential expression (DE) results