check out what is XenaR and http://www.cancergenomics.net/multiomics.html

[souravsingh]

@jingchunzhu I have installed the XenaR package and will be able to give the feedback on the package soon.

[jingchunzhu]

@souravsingh great. looking forward to the update.

[souravsingh]

I have taken a look at the XenaR package and here is what I think- XenaR is a good client library for UCSC Xena to query various datasets available in UCSC Xena and retrieve them directly in matrix format without preprocessing. It doesn't contain any kind of visualization features that the UCSC Xena client library contains, which can be a bummer.

[jingchunzhu]

@souravsingh Thanks for the summary. It is fine that XenaR does not provide viz (and perhaps a good idea) -- likely it just serves the function of pulling external public data (in this case on xena) to R environment, and then analysts decide what analysis to run on these data, and use their existing visualization tool or code for viewing their analysis results.

[souravsingh]

The library can come really handy for the Pathway Perturbation project since the library can query and access the data directly in matrix format. So it can be used for quick prototyping of statistical tests for pathway perturbation.

[souravsingh]

@jingchunzhu I will also look into the multiomics tool

[souravsingh]

@jingchunzhu The multiomics tool could be handy for the Pathway perturbation since it can identify the paired features between the mRNA and the methylation profiles and the possible interactions.