tag:userecho.com,2024-03-29:/feeds/topics/en//DeepBlue Epigenomic Data Server2019-10-23T07:15:53+00:00tag:deepblue.userecho.com,2019-10-23:/communities/1/topics/78-45451/2019-10-23T07:15:53+00:002019-10-23T07:15:53+00:0045451 [ideas] <br/><br/>suggested by: AnonymousAnonymoustag:deepblue.userecho.com,2019-10-23:/communities/1/topics/77-kiol/2019-10-23T05:06:08+00:002019-10-23T05:06:08+00:00kiol [ideas] <p></p><p><img src="/s/attachments/15013/1/0/c9c2e05acd79775e70290a6459d7d78f.jpg"></p><br/><br/>suggested by: AnonymousAnonymoustag:deepblue.userecho.com,2019-10-23:/communities/1/topics/76-ihkjkjb/2019-10-23T04:46:28+00:002019-10-23T04:46:28+00:00ihkjkjb [ideas] <p><img src="/s/attachments/15013/1/0/fb160678326de779ec48b98e4c654ecd.jpg"></p><br/><br/>suggested by: AnonymousAnonymoustag:deepblue.userecho.com,2019-02-24:/communities/1/topics/43-is-the-server-down/2019-02-24T13:10:17+00:002019-02-24T13:10:17+00:00is the server down? [ideas] <p>Is deepBlue still working or is the servicedown?</p><br/><br/> Felipe Albrecht replied:<br/><p>Hello,</p><p>sorry for the delay.</p><p>No, the server wasn't down during this period.</p><p></p><p>Thank you for asking,</p><p>Felipe Albrecht<br></p>Anonymoustag:deepblue.userecho.com,2018-06-05:/communities/1/topics/42-would-it-be-possible-to-access-roadmap-epigenomics-complete-data/2018-06-05T15:55:59+00:002018-06-05T15:55:59+00:00Would it be possible to access Roadmap epigenomics complete data? [ideas] <p>Hi,</p><p><br></p><p>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. </p><p><br></p><p>I am working on breast and I used CEEHRC data for individual cells types. </p><p><br></p><p>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! </p><p><br></p><p>Thanks</p><p><br></p><p>Melanie</p><br/><br/>suggested by: Melanie BusbyMelanie Busbyhttps://deepblue.userecho.com/users/40-melanie-busby/topics/tag:deepblue.userecho.com,2017-06-21:/communities/1/topics/41-lock-selection-in-experiments-grid/2017-06-21T07:24:58+00:002017-06-21T07:24:58+00:00Lock selection in Experiments grid [ideas] <p>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.</p><p><br></p><p>Example:</p><p><br></p><p>Select cellA through cellZ (lock)</p><p>Select various TFs -> create request</p><p>Clear selected TFs</p><p>Select various histone modifications -> create request</p><p>Clear selected HMs</p><p><br></p><p>Example 2:</p><p>Select cellA through cellZ (lock)</p><p>Select various histone modifications (lock)</p><p>Select project A -> create request</p><p>Clear project A</p><p>Select project B -> create request</p><br/><br/>suggested by: AnonymousAnonymoustag:deepblue.userecho.com,2017-06-09:/communities/1/topics/40-build-a-matrix-of-methylation-levels-from-rrbs-encode/2017-06-09T07:21:32+00:002017-06-09T07:21:32+00:00build a matrix of methylation levels from RRBS ENCODE [questions] <p>Hi Felipe,</p><p><br></p><p>I'm posting my question here again as you suggested.</p><p>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.</p><p><br></p><p>what is the easiest way to do it in DeepBlue? in R environment would be the best.</p><p> </p><p>Best,</p><p>Abdul</p><p><br></p><br/><br/> DeepBlue Data Server replied:<br/><p>Hello, thank you for the question:</p><p><em><br></em></p><p><em>"How to build a matrix summarizing methylation level of every possible CpG covered resolution from RRBS data of ENCODE (only from tissues and primary cell, hg19 genome)."</em></p><p><br></p><p>Firstly, you have to list all RRBS experiments from ENcODE:</p><p><em>encode_rrbs <- deepblue_list_experiments(technique = "RRBS", project = "ENCODE")</em></p><p><br></p><p>Extract their IDs:</p><p><em>encode_rrbs_names <- deepblue_extract_names(encode_rrbs )</em></p><p>Select the columns where the aggregation will be performed: <br><em>exp_columns <- deepblue_select_column(encode_rrbs_names, "SCORE")</em></p><p><br></p><p>Find all CGs in the hg19 genome: (here, we are selecting only the chromosome 21):<br><em>cgs_hg19 <- deepblue_find_motif(motif="CG", genome="hg19", chromosomes="chr1") </em></p><p>This command will return a query ID, that “contains” all genomic coordinates where the pattern/motif “CG” appear.<br>Important remark: Do each chromosome separately. This kind of operation can be slow… we are talking about more than 200 samples, getting millions of regions of each one… so, do not be greedy.<em>do not be greedy.</em></p><p><br></p><p>Building the score matrix:<br><em>deepblue_score_matrix(<br> experiments_columns=experiments_columns,<br> aggregation_function="mean", aggregation_regions_id=cgs_hg19</em></p><p><em>)</em><br><br>Use the command deepblue_download_request to download the data:<em><br>e.g. score_matrix <- deepblue_download_request_data(request_id = request_id)</em></p><p><br></p><p>And the command deepblue_export_tab to save the data:<br><em>deepblue_export_tab(score_matrix, target.directory = "./", "cgs_methylation")</em></p><p><br></p><p>Please, look at <a href="http://bioconductor.org/packages/release/bioc/manuals/DeepBlueR/man/DeepBlueR.pdf">http://bioconductor.org/packages/release/bioc/manuals/DeepBlueR/man/DeepBlueR.pdf</a> for a complete reference of all commands provided by DeepBlueR.</p><p><br></p><p>As reference, here is the full code:</p><p></p><p><em>library(DeepBlueR)<br><br></em></p><p><em>encode_rrbs <- deepblue_list_experiments(technique = "RRBS", project = "ENCODE")<br><br></em></p><p><em>exp_columns <- deepblue_select_column(encode_rrbs, "SCORE")<br><br></em></p><p><em>cgs_hg19 <- deepblue_find_motif(motif="CG", genome="hg19", chromosomes="chr1")<br><br></em></p><p><em>status <- deepblue_score_matrix(</em></p><p><em> experiments_columns=exp_columns, </em></p><p><em> aggregation_function="mean", </em></p><p><em> aggregation_regions_id=cgs_hg19</em></p><p><em>)<br>score_matrix <- deepblue_download_request_data(request_id = request_id)<br>deepblue_export_tab(score_matrix, target.directory = "./", "cgs_methylation")</em></p><p><em></em></p><p><br></p>Abdulrahman Salhabhttps://deepblue.userecho.com/users/39-abdulrahman-salhab/topics/tag:deepblue.userecho.com,2017-03-30:/communities/1/topics/1-beautiful-design/2017-03-30T13:44:06+00:002017-03-30T13:44:06+00:00Beautiful Design. [praises] [thanks]<p>Beautiful design</p><br/><br/> deepblue replied:<br/>Anonymoustag:deepblue.userecho.com,2017-03-30:/communities/1/topics/3-methylation-array-data/2017-03-30T13:43:57+00:002017-03-30T13:43:57+00:00Methylation array data [ideas] [under review]<p>Are there plans to add consortium data from Illumina Infinium methylation arrays? Nice work with this so far!</p><br/><br/> deepblue replied:<br/>Anonymoustag:deepblue.userecho.com,2017-03-30:/communities/1/topics/6-how-can-i-use-deepblue-to-query-encode-rnaseq-at-a-gene-level/2017-03-30T13:43:30+00:002017-03-30T13:43:30+00:00How can I use DeepBlue to query ENCODE RNAseq at a gene-level? [questions] [under review]<p>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: <a href="https://www.encodeproject.org/files/ENCFF833DWB/">https://www.encodeproject.org/files/ENCFF833DWB/</a>.<br></p><p><br></p><p>Can these be searched using DeepBlue?<br></p><br/><br/> deepblue replied:<br/>floris barthelhttps://deepblue.userecho.com/users/6-florisbarthel/topics/tag:deepblue.userecho.com,2017-03-30:/communities/1/topics/5-missing-signal-values/2017-03-30T13:43:12+00:002017-03-30T13:43:12+00:00Missing Signal Values [questions] [answered]<p>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.</p><p><br></p><p>R code:</p><p>`</p><p><span style="background-color: initial;">id <- deepblue_select_experiments(experiment_name = "E050_WGBS_ReadCoverage.bedgraph", chromosome = "chr6", start=26330464, end=26330664)</span></p><p>request <- deepblue_get_regions(query_id = id, output_format = "CHROMOSOME,START,END,SIGNAL_VALUE")<span><br></span></p><p><span><span>region <- deepblue_download_request_data(request_id = request)<br></span></span></p><p><span><span><span>region<br></span></span></span></p><p><span><span><span>`</span></span></span></p><p><span><span><span>Result:</span></span></span></p><p><span>`</span></p><p>Called method: deepblue_select_experiments<br></p><p><span></span></p><pre><span class="ace_constant ace_language">Reported status was: okayCalled method: deepblue_get_regionsReported status was: okayCalled method: deepblue_infoReported status was: okayCalled method: deepblue_infoReported status was: okaytrying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r791736&key=anonymous_key'Content type 'application/x-bzip2' length 124 bytes==================================================downloaded 124 bytesDecompressing downloaded file to /tmp/RtmpZfobRp/file495c5e0585df_uncompressReading 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</pre><p><span>`</span></p><p><br></p><p><span>Bedfile downloaded from the web interface open in IGV:</span></p><p><span><img src="/s/attachments/15013/1/5/8b597cc29a6c7d7be191d63abdfb1b82.png"><br></span></p><p><span><br></span></p><p><span>Any Suggestions?<span><br></span></span></p><p></p><br/><br/> deepblue replied:<br/>Richard Actonhttps://deepblue.userecho.com/users/5-richard-acton/topics/tag:deepblue.userecho.com,2017-03-30:/communities/1/topics/7-query-metadata-based-on-encode-accession-ids-deepbluer/2017-03-30T13:42:49+00:002017-03-30T13:42:49+00:00Query metadata based on ENCODE accession IDs (DeepBlueR) [questions] [answered]<p>Hi, I'm interested to use DeepBlue to fetch ENCODE metadata based on the accesssion IDs. </p><p><br></p><p>Eg. ENCSR000AEH, ENCSR000AEF<span>, ENCSR000AED</span></p><p><br></p><p>This can be done in the package ENCODExplorer but I could not find such features in DeepBlueR. <a href="https://www.bioconductor.org/packages/release/bioc/html/ENCODExplorer.html">https://www.bioconductor.org/packages/release/bioc/html/ENCODExplorer.html</a><br></p><br/><br/> deepblue replied:<br/>floris barthelhttps://deepblue.userecho.com/users/6-florisbarthel/topics/tag:deepblue.userecho.com,2016-11-11:/communities/1/topics/4-double-clicking-isnt-remove-a-selected-item/2016-11-11T17:49:34+00:002016-11-11T17:49:34+00:00Double clicking isn't remove a selected item [bugs] <p>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.<br></p><br/><br/> DeepBlue Data Server replied:<br/><p>Hello, I tested in the grid page and the experiments table and it is working as expected.</p><p>May you give more information or how to better test this issue?</p><p><br></p><p>Thank you</p>Anonymoustag:deepblue.userecho.com,2015-08-06:/communities/1/topics/2-simplify-addition-of-project-datasets/2015-08-06T21:54:54+00:002015-08-06T21:54:54+00:00Simplify addition of project datasets [ideas] [completed]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<br/><br/> deepblue replied:<br/>Anonymous