This repository houses the custom code used to analyze data and generate figures within the manuscript entitled "Genomic insights into the pediatric obese asthma phenotype reveal a shift to memory T cells and cellular reprogramming targeting Rho GTPase pathways."
The code is broken into five main categories with respective folders:
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Annotations The code used to annotate enhancers within the study as well as link CpGs (and me-CpGs) to their respective gene (me-genes).
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Genotyping The code used to call and perform quality control on genetic variants from illumina MEGA and then curate genetic, gene expression, and DNA methylation datasets to perform eQTL and mQTL analyses.
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Gene_Expression The code used to determine differentially expressed genes between normal weight and obese asthmatic children.
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DNA_Methylation The code used to determine differentially methylated CpGs between normal weight and obese asthmatic children.
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Cell_Subtype_Proportions The code used to determine cell subtype proportion differences between normal weight and obese asthmatic children.