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2024_gtex_smoking's Introduction

Companion Github Repository for the paper "The molecular impact of cigarette smoking resembles aging across tissues"

Getting the code

git clone https://github.com/Mele-Lab/2024_GTEx_Smoking.git

Software dependencies

Package Version Packages Version
edgeR 4.0.16 dplyr 1.1.4
optparse 1.7.5 limma 3.58.1
missMethyl 1.38.0 ggplot2 3.5.0
reshape2 1.4.4 caret 6.0-94
hier.part 1.0-6 sandwich 3.1-0
multcomp 1.4-25 lmtest 0.9-40

Running the code

Code to run differential gene expression analysis

/analysis/Expression_models.sh

Code to run differential splicing analysis

/analysis/Splicing_models.sh

Code to run differential methylation analysis

/analysis/Methylation_models.sh

Code to run enrichement analsyis on gene expresion results

/analysis/Enrichement_analysis.sh

All expected output is available as supplementary tables in the paper

2024_gtex_smoking's People

Contributors

jmiguelramirez avatar zroger49 avatar

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