# Interactive Shiny App for Bulk Sequencing Data

## Documentation for package ‘bulkAnalyseR’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
genes_barplot | Create a bar plot of expression for selected genes across samples in an experiment
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
qc_density_plot | Create a density plot of log2 expression across samples of an experiment
qc_violin_plot | Create a violin/box plot of expression across samples of an experiment
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
scatter_plot | Create a scatter plot of expression between two samples of an experiment
volcano_enhance | Create a volcano plot visualising differential expression (DE) results
volcano_plot | Create a volcano plot visualising differential expression (DE) results