A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

This repository contains all the scripts necessary for producing the results of the manuscript, for which a preprint is available at:

Raw data is also available at:

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List of reproducible pipelines and other repositories developed as part of this project:

• Differential gene expression analysis: The Salmon-tximport-DESeq2 pipeline
• Differential RNA stability analysis: The STAR-featureCounts-REMBRANDTS-limma pipeline
• Integrated methods for meRIP-seq data analysis – https://github.com/abearab/imRIP
• Pathway analysis using PAGE algorithm and downstream analysis – https://github.com/abearab/pager
• Scripts for mapping NGS reads to HERVs – https://github.com/abearab/HERVs

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This repo has been developed in Gilbert at UCSF and Arc Institute by Abolfazl Arab, in collaboration with Goodarzi lab at UCSF. This also incldue some original/revised codes from Alex Y. Ge, Hosseinali Asgharian, and Hani Goodarzi.