Examples of visualization and analysis of the enrichment and epigenomic similarity results

R.genomerunner is currently developed in shiny branch

Scripts for processing the enrichment analysis matrixes produced by GenomeRunner Web or GenomeRunner. The scripts are developed in, and best used with RStudio

• Analysis.Rmd and Analysis.html - The main tutorial for the enrichment and regulatory similarity analyses and visualization in R.

• Analysis_v2.Rmd and Analysis2.html - The main tutorial with steps automated using utils2.R and episimilarity.R auxillary functions.

• Enrichment_analysis.Rmd and Enrichment_analysis.html - Demonstration of the ideas for visualization of the enrichment results.

• episimilarity.R - Functions for plotting, differential analyses, cell type enrichment analysis.

• genomeRunner_file_formatting_functions.R - Functions 'getV1...' and 'getV2...' that process LOG and detailed output of GenomeRunner, respectively, into standardized matrixes 'matrix_OR.txt' and 'matrix_PVAL.txt'. These matrixes of odds ratios and p-values are then utilized by the utils2.R and episimilarity.R functions.

• genomeRunner_file_formatting_functions2.R - Version 2 of the above functions that includes proper odds ratios handling.

• utils.R - Functions used by main scripts. Main function plotting tme majority of the results.

• utils1.R - Version 1 of the main function that treats the results from same cell-factor experiments from different institutions as replicates, and plots the most significant results.

• utils2.R - Version 2 of the main 'showHeatmap' function, data load and other helper functions.

• 01_heatmap_corr.R - Code snippets to perform enrichment- and regulatory similarity analyses clustering and visualization, as well as some exploratory tests.