DNA methylation integrated package

Question

[forever]

I find a lot of software for DNA methylation analysis in the below link: A: Gallery: Computational tools for DNA methylation

DNA methylation needs 5 stages:

Mapping and Normalization
Preprocessing
Analysing
Visualisation
Validation and interpretation

Partek company has a software for all these stages but it is not free.

My question is:

1- Which of the current packages have the five stages with different options?

2- I need a tutorial to follow to reproduce some figures like?

Thank you

[German.M.Demidov]

https://rnbeads.org ?

Answer 1

[mario.red8976]

Hi! I suggest, if It's possible, to find a bioinformatician that can do it for you or learn by yourself how do to it using R programming and bioconductor. In a similar topic (A: Appropriate Pipeline for Methylation EPIC array analysis? ) I suggested an user to follow this tutorial: https://www.bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html . You need to know how to write code in R and install bioconductor packages etc.. Hope it helps, check it out!

[Rut_MDLV]

Hi, I agree with the above mentioned, minfi is a good methylation specific package that includes normalization and quality control while limma allows testing for differential methylation. They work well together and are easy to adapt to your necessities. I use missMethyl: Analysing Illumina HumanMethylation BeadChip Data for the enrichment. They incorporate a batch correction method that works pretty good (consider other methods, e.g. combat too). Integrates nice with minfi and limma and good for visualization too. I hope this enhances the previous response!