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:
Raw data is also available at:
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
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.