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Under review

Methylation array data

Anonymous 2 years ago • updated by deepblue 10 months ago 2

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


build a matrix of methylation levels from RRBS ENCODE

Abdulrahman Salhab 8 months ago • updated by DeepBlue Data Server 8 months 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.





Query metadata based on ENCODE accession IDs (DeepBlueR)

floris.barthel 10 months ago • updated by deepblue 10 months ago 7

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


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

Under review

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

floris.barthel 10 months ago • updated by deepblue 10 months 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?


Beautiful Design.

Anonymous 2 years ago • updated by deepblue 10 months ago 2

Beautiful design


Lock selection in Experiments grid

Anonymous 7 months ago 0

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.


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


Missing Signal Values

Richard Acton 12 months ago • updated by deepblue 10 months ago 4

I am having some trouble downloading data in the R API/package. It all seems to work fine but I am not getting any signal values. If I download this same data as a bed file there are signals in this range of positon values, but if I download it in R I don't get any values in the signal value column.

R code:


id <- deepblue_select_experiments(experiment_name = "E050_WGBS_ReadCoverage.bedgraph", chromosome = "chr6", start=26330464, end=26330664)

request <- deepblue_get_regions(query_id = id, output_format = "CHROMOSOME,START,END,SIGNAL_VALUE")

region <- deepblue_download_request_data(request_id = request)





Called method: deepblue_select_experiments

<span class="ace_constant ace_language">Reported status was: okay
Called method: deepblue_get_regions
Reported status was: okay
Called method: deepblue_info
Reported status was: okay
Called method: deepblue_info
Reported status was: okay
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r791736&key=anonymous_key'
Content type 'application/x-bzip2' length 124 bytes
downloaded 124 bytes

Decompressing downloaded file to /tmp/RtmpZfobRp/file495c5e0585df_uncompress
Reading file from /tmp/RtmpZfobRp/file495c5e0585df_uncompress
</span>GRanges object with 18 ranges and 1 metadata column:
       seqnames               ranges strand | SIGNAL_VALUE
          <Rle>            <IRanges>  <Rle> |  <character>
   [1]     chr6 [26330521, 26330522]      * |             
   [2]     chr6 [26330522, 26330523]      * |             
   [3]     chr6 [26330544, 26330545]      * |             
   [4]     chr6 [26330545, 26330546]      * |             
   [5]     chr6 [26330552, 26330553]      * |             
   ...      ...                  ...    ... .          ...
  [14]     chr6 [26330602, 26330603]      * |             
  [15]     chr6 [26330603, 26330604]      * |             
  [16]     chr6 [26330604, 26330605]      * |             
  [17]     chr6 [26330644, 26330645]      * |             
  [18]     chr6 [26330645, 26330646]      * |             
  seqinfo: 1 sequence from an unspecified genome; no seqlengths


Bedfile downloaded from the web interface open in IGV:

Any Suggestions?


Double clicking isn't remove a selected item

Anonymous 1 year ago • updated by DeepBlue Data Server 1 year ago 1

After filtering and clicking on a particular dataset if I want to remove the unwanted data it isn't removing by double clicking even though it is mentioned above as such. Please fix the problem.


Simplify addition of project datasets

Anonymous 3 years ago • updated by deepblue 2 years ago 1
Provide a function that takes a list of project specific IDs and add these datasets automatically based on the metadata already available for these files