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the GRIN2 Package", "author": "Abdelrahman Elsayed, PhD and Stanley Pounds, PhD", "engine": "knitr::rmarkdown", "headings": [ "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:", 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