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 |