This repository contains the code and pre-processed data used in the study of tissue- and time-specific DNA methylation dynamics in Sus scrofa via joint fused ridge network modeling.
To clone the repo use git clone https://github.com/wachalak/methylation-networks.git
The Code directory contains two files: pre_processing.sh and analyses.R
- pre_processing.sh gives the workflow to obtain bed files needed for the analyses with R. The initial data used in this study were collected by the GENE-SWitCH (https://www.gene-switch.eu/), and are available through the FAANG data portal at https://data.faang.org/projects/GENE-SWitCH. The accession code is: (i) PRJEB41822 for RRBS; (ii) PRJEB41970 for RNA-Seq; and (iii) PREJEB70458 for ChIP-Seq
- analyses.R gives the complete workflow for joint fused ridge network modeling and analysis
The Data-post-processing directory contains all files needed to run analyses.R. The bed files have been compressed. To decompress all bed files in the directory you can run either:
gunzip *.bed.gz, orfor file in *.bed.gz; do bgzip -d "$file"; done
For questions or feedback, please contact:
- Author: Karolina Wachala
- Email: karolina.wachala@unibe.ch
This repository is licensed under the MIT License. See the LICENSE file for more details.