help

[Khonaw Klader]

Good morning 

every one 

I am a PhD student, and I am new to the bioinformatics field. Who can guide how I  query the data from cBioportal.org?  My project is about epigenetic modification (DNA methylation and RNA methylation).

  Who can help with R programming, Galaxy, and how to bring data from CBioPortal to R programming and Galaxy  for data analysis and interpretation  

[Guizela Huelsz Prince]

Hello!

cBioPortal focuses mainly on somatic mutations, copy-number alterations, mRNA / protein expression, and clinical data. It only includes limited gene-level DNA methylation in a few studies, and no RNA methylation, so it might not be the ideal source for epigenetic data. That said, you can still use cBioPortal for genomic + clinical context, pull data into R, and combine it later with methylation data from other sources

To work with cBioPortal data in R, the cBioPortalData package is the easiest option. In Galaxy, you can upload TSV/CSV files downloaded from cBioPortal and use standard tools for filtering, merging, and visualization.

Best,

Guizela