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Under review

Methylation array data

Anonymous 5 years ago updated by deepblue 4 years ago 2

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

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build a matrix of methylation levels from RRBS ENCODE

Abdulrahman Salhab 4 years ago updated by DeepBlue Data Server 4 years ago 1

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


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Answered

Query metadata based on ENCODE accession IDs (DeepBlueR)

floris.barthel 4 years ago updated by deepblue 4 years ago 7

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

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Under review

How can I use DeepBlue to query ENCODE RNAseq at a gene-level?

floris.barthel 4 years ago updated by deepblue 4 years ago 3

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?

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Thanks

Beautiful Design.

Anonymous 5 years ago updated by deepblue 4 years ago 2

Beautiful design

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45451

Anonymous 1 year ago 0
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kiol

Anonymous 1 year ago 0

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ihkjkjb

Anonymous 1 year ago 0

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is the server down?

Anonymous 2 years ago updated by Felipe Albrecht 2 years ago 1

Is deepBlue still working or is the servicedown?

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Would it be possible to access Roadmap epigenomics complete data?

Melanie Busby 3 years ago 0

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