Interactive Shiny App for Bulk Sequencing Data

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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