how to analyse methylation data from GEO?
how to analyse methylation data from GEO?
can GEO2R be used for methylation data if it is available?
please suggest
Thanks
methylation
geo
geo2r
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Your first question is very large, there are many approaches depending on the methods used to obtain the methylation data, and you will certainly find useful tutorials on internet GEO2R can be used to analyzed methylation data but it might be limited if you want to do in-depth analysis such as differentially methylated regions