bulkAnalyseR1.1.0 package

Calculate statistics for each gene of an expression matrix given a gro...

Create a cross plot comparing differential expression (DE) results

Generate the cross plot panel of the shiny app

Perform differential expression (DE) analysis on an expression matrix

Generate the DE panel of the shiny app

Generate the DE plot plot panel of the shiny app

Generate the DE summary panel of the shiny app

Determine the pattern between two intervals

Generate the enrichment panel of the shiny app

Create heatmap of an expression matrix

Find recurring regulators

Generate all files required for an autonomous shiny app

Create a bar plot of expression for selected genes across samples in a...

Convert the adjacency matrix to network links

Generate the GRN cis integration panel of the shiny app

Generate the GRN custom integration panel of the shiny app

Generate the GRN panel of the shiny app

Generate the GRN trans integration panel of the shiny app

Perform GRN inference

Create a heatmap of the Jaccard similarity index (JSI) between samples...

Calculate the Jaccard similarity index (JSI) between two vectors

Generate the landing page panel of the shiny app

Create an MA plot visualising differential expression (DE) results

Create a matrix of the average expression of each gene in each conditi...

Create a matrix of the patterns between conditions

Generate an app panel for a modality

Apply a modified noisyR counts pipeline printing a plot

Generate the expression patterns panel of the shiny app

Pipe operator

Plot a GRN

Create a line plot of average expression across conditions

Create a principal component analysis (PCA) plot the samples of an exp...

Visualise the overlap of edges between different networks

Creates a comparison table for miRTarBase to be used for custom integr...

Pre-process the expression matrix before generating the shiny app

Create a density plot of log2 expression across samples of an experime...

Create a violin/box plot of expression across samples of an experiment

Generate the QC panel of the shiny app

Rescale a matrix

Generate the sample select panel of the shiny app

Create a scatter plot of expression between two samples of an experime...

Create a volcano plot visualising differential expression (DE) results