Introduction | T-ALL Example dataset | 1) Obtain clinical, lesion and gene expression data | 2) Retrieve Genomic Annotations for Genes and Regulatory Features | 3) Retrieve Chromosome Size Data | 4) Run Genomic Random Interval (GRIN) Analysis | 5) Now, let's Take a Look on the GRIN Output Results: | 6) Write GRIN Results | 7) Genome-wide Lesion Plot | 8) Stacked Barplot for a List of Genes of Interest | 9) Prepare GRIN Lesion Matrix for an OncoPrint Type of Display | 10) Lesion Plots for a Certain Gene, Locus or the Whole Chromosome | 11) Gene-Lesion Matrix for later computations | Associate Lesions with EXpression (ALEX) | 12) Prepare Expression and Lesion Data for ALEX-KW Test and ALEX-plots | 13) Run Kruskal-Wallis Test for Association between Lesion and Expression Data | 14) Now, let's Take a Look on the ALEX Kruskal-wallis Results Table: | 15) Waterfall Plots for Side-by-side Representation of Lesion and Expression Data | 16) Visualize Lesion and Expression Data by Pathway (JAK/STAT Pathway) | 17) Lesion Binary Matrix for Association Analysis with Clinical Outcomes | 18) Run Association Analysis for Lesions with Clinical Outcomes | 19) Now, let's Take a Look on the Results Table of the Association between Lesions and Treatment Outcomes: