Add DIMMER for methylation

[nictru]

Please describe what we should use this tool for and how we can put this in our pipeline

Some potentially interesting resources:

• Paper
• Website

[mlist]

Since the original publication by the Baumbachlab, Dimmer has been significantly extended by Manuela Lautizi, @JohannesKersting and @alex-d13 among others. It now has considerably more features. The main purpose of the tool is to dynamically identify regions of DNA that are differentially methylated between conditions. Such DMRs may hold relevant TFBS. During the meeting Martin Hirst pointed out to us how important DMRs are for TF activity changes (possibly even more so than other epigenetic signales) which is why we wanted to include DIMMER here for identifying regions of interest for further analysis.

[nictru]

I have just looked at the documentation and discovered that at least the SDU version takes IDAT files as input, which apparently is a specialized Illumina raw data format which presumably is not available to most users. Starting from wig/signal files would probably be more user friendly. Unfortunately I could not find documentation for the updated version of @JohannesKersting, maybe something like this has already been implemented?

[nictru]

Here some notes on a potential implementation:

• The STARE input regions are determined per condition and assay, so we cannot really use the differential methylation information here, except if we identify the differentially methylated regions with all other conditions and proceed with a union/intersection of the identified enhancer regions
• We could potentially consider this information in the scoring/ranking part of the pipeline, but I don't know enough about the output information of Dimmer and the biological perspective
• We could add this information to the report in some way

[Firestar93]

We should talk to Johannes for this issue.

[JohannesKersting]

The current version of Dimmer also supports beta-values matrices in CSV format as input. The SDU version is quite outdated. I will mail you a more up-to-date version of the manual.