Are there plans to add consortium data from Illumina Infinium methylation arrays? Nice work with this so far!

Hi Felipe,

I'm posting my question here again as you suggested.

I want to build a matrix summarizing methylation levels at CpGs resolution from RRBS data of ENCODE (only from tissues and primary cell, hg19 genome), so that I get the methylation level of every possible CpG covered by one sample (or more). and then download this matrix and save to a file.

what is the easiest way to do it in DeepBlue? in R environment would be the best.

Best,

Abdul

Hi, I'm interested to use DeepBlue to fetch ENCODE metadata based on the accesssion IDs.

Eg. ENCSR000AEH, ENCSR000AEF, ENCSR000AED

This can be done in the package ENCODExplorer but I could not find such features in DeepBlueR. https://www.bioconductor.org/packages/release/bioc/html/ENCODExplorer.html

I'm interested to get gene-level expression counts/TPMs for ENCODE datasets? Can this be done using DeepBlue? For example, there are matrices found here: https://www.encodeproject.org/files/ENCFF833DWB/.

Can these be searched using DeepBlue?

Beautiful design

Is deepBlue still working or is the servicedown?

Hi,

Thank you so much for DeepBlueR that makes it much easier to newbies like be to get familiar with all the data accessible through the project included here. 

I am working on breast and I used CEEHRC data for individual cells types. 

Now I would also like to access data from Roadmap Epigenomics but the only cell types available are HMEC and myoepithelial cells that were included in the publication. However, there is also data for luminal cells, fibroblasts and stem cell I they are not accessible through DeepBlue. Would it be possible to make it accessible? Would be great! 

Thanks

Melanie

Assuming I want to select different assays for the same set of cell types, or the same assays for the same cell types for different projects. I could create a huge request resulting in one file that I have to split later locally; a more convenient way could be to lock certain selections in the experiment grid and create separate requests.

Example:

Select cellA through cellZ (lock)

Select various TFs -> create request

Clear selected TFs

Select various histone modifications -> create request

Clear selected HMs

Example 2:

Select cellA through cellZ (lock)

Select various histone modifications (lock)

Select project A -> create request

Clear project A

Select project B -> create request