Combining DNA methylation with bulk RNA sequencing to profile molecular pattern of chordomas

This repository documents work, described in Acta Neuropathologica Communications publication DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment.
Please note, that this publication utilizes molecular data, obtained from our patients. They trusted us with their private data. Therefore, we have decided against publishing raw .fastq and .idat files as they contain SNPs and could be potentially used identify them or their family members. However, normalized and anonymized data are available through Gene Expression Omnibus GSE230168.
In order to reproduce our results, you can use minfi::getGenomicRatioSetFromGEO(GSE = "GSE230168") to get GenomicRatioSet. To get RNAseq counts are available in chordoma_counts.csv table.