tag:userecho.com,2024-03-29:/feeds/topics/ca//EpiExplorer2021-05-20T13:04:47+00:00tag:epiexplorer.userecho.com,2021-05-20:/communities/1/topics/787-hallo-thank-you-for-developing-and-sharing-these-useful-tool-i-am-very-new-in-this-field-so-i/2021-05-20T13:04:47+00:002021-05-20T13:04:47+00:00Hallo! Thank you for developing and sharing these useful tool! I am very new in this field, so I started by following your tutorial, and I have obtained very interesting results in the study of the Differentially methylated regions that I am studying. I [preguntes] <p>Hallo!</p><p>Thank you for developing and sharing these useful tool! I am very new in this field, so I started by following your tutorial, and I have obtained very interesting results in the study of the Differentially methylated regions that I am studying.</p><p>I contact you because yesterday, after about a month, I needed to process new data but I was unable to use epiexplorer nor to load new data. I am attaching the screen photo to show the error message I see. Could you please help me to understand if I do something wrong or inform me if the webtool is not working?</p><p>Thanks in advance.</p><p>Maria Tropea</p><p>University of Catania, Sicily</p><p><br></p><ul></ul><br/><br/>Suggerit per: Maria TropeaMaria Tropeahttps://epiexplorer.userecho.com/users/737-maria-tropea/topics/tag:epiexplorer.userecho.com,2019-05-24:/communities/1/topics/753-finansyi/2019-05-24T05:02:30+00:002019-05-24T05:02:30+00:00Финансы. [preguntes] <br/><br/>Suggerit per: АлексейАлексейhttps://epiexplorer.userecho.com/users/678-aleksej/topics/tag:epiexplorer.userecho.com,2016-06-24:/communities/1/topics/96-mouse-mm10-genome/2016-06-24T09:50:45+00:002016-06-24T09:50:45+00:00Mouse mm10 genome [idees] <p>Would it be possible to get the mouse mm10 genome available?</p><br/><br/>Suggerit per: elisa redlelisa redlhttps://epiexplorer.userecho.com/users/13-elisaredl/topics/tag:epiexplorer.userecho.com,2015-06-08:/communities/1/topics/33-same-start-and-end-position/2015-06-08T16:06:40+00:002015-06-08T16:06:40+00:00same start and end position [preguntes] I am a new user. I performed targeted bisulfite sequencing on 2 groups of samples and subsequently analyzed the data with Methylkit in R. My output file is a list of CpGs significantly differentially methylated between the 2 groups, with the 3 columns as requested by the EpiExplorer program (chr, start, end). My data is at single CpG level, thus start and end positions are exactly the same. This gives an error when uploading the file: "<h4>Error: Invalid format at line 0. chromosome end(843641) should be larger than chromosome start (843641)"</h4><br><br><br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2013-11-01:/communities/1/topics/31-export-of-control-regions/2013-11-01T13:36:46+00:002013-11-01T13:36:46+00:00Export of control regions [preguntes] Great tool. Any chance to get an export function for the matched control regions that are generated by epiexplorer?<br><p><br></p><br/><br/> Mario Saare replied:<br/><p>Hi! <br></p><p> I would like to combine the % of overlapping regions retrieved from EpiExplorer and the statistical significance found with Genomic HyperBrowser. However, the HyperBrowser does not give the % of overlaps of the control regions (random regions that are generated to calculate the null distribution). EpiExplorer gives this %, but I couldn't find how are the control regions calculated. From the region lengths plots I can see that the control regions have the same length distribution as my data, but what about the gaps between regions? Are these preserved as well? Then I would know which 'preservation rule' to pick in the HyperBrowser so that it would randomize the positions in the same way.</p><p>Best regards,</p><p>Mario<br></p>Anònimtag:epiexplorer.userecho.com,2013-10-14:/communities/1/topics/51-methylation-thresholds/2013-10-14T19:25:19+00:002013-10-14T19:25:19+00:00methylation thresholds [preguntes] <p></p><p></p><div><div><div><p>Dear Konstantin, I have a related question. I have been exporing the original methylation files and was wondering which thresholds does EpiExplorer use for read coverage and percentage of reads with methylation. In UCSC they recommend requiring at least 10 reads and they assign colors depending on what fraction of the reads is found to be methylated.</p><p>Thanks again,</p><p>Federico</p></div></div></div><p></p><div><div><div><div><p></p></div></div></div></div><br><p></p><br/><br/> Halachev replied:<br/><p>Dear Federico,</p><p><br></p><p>In the summary methylation plot, we discussed, EpiExplorer takes into consideration only the methylation ratio. Keep in mind that this plot is only intended to provide intuition about the data. <br></p><p><br></p><p>In case, you want to inspect after you apply additional filters, I suggest you filter out your regions for number of CpGs (and/or coverage) and then you can inspect the details of the distribution of methylation ratios. <br></p><p><br></p><p>You can see an example here: <a href="http://www.slideshare.net/khalachev/step-by-step-guide-to-figure-1">http://www.slideshare.net/khalachev/step-by-step-guide-to-figure-1</a></p><p>slide 8</p><p><br></p><p>best,<br></p><p>Konstantin<br></p>Federico Abascalhttps://epiexplorer.userecho.com/users/10-federico-abascal/topics/tag:epiexplorer.userecho.com,2013-10-10:/communities/1/topics/25-methylation-chart/2013-10-10T14:33:09+00:002013-10-10T14:33:09+00:00Methylation chart [preguntes] <p>Dear colleagues,</p><p>I am comparing a bed of exons against the corresponding full-genes bed file. By looking at "DNA methylation (ENCODE)" I can see higher bars for full-genes (e.g. 75% unmethylated for genes compared to 5% unmethylated for exons). </p><p><br></p><p>Below, it can be read: </p><table><tbody><tr><td><p><b>Chart description:</b> The bar chart visualizes the percentage of regions in the selected region set that overlap with any of the listed genomic and epigenomic features on the x-axis.</p></td></tr></tbody></table>And this is what I do not understand. The plot suggests more methylation on exons, but the chart description refers to percentages of regions that overlap with a given epigenomic feature. Then, if an exon intersects with a methylated region, then the corresponding gene should intersect too. What am I missing here?<p></p><p><br></p><p>Many thanks for EpiExplorer, it is really helpful,</p><p>Best,</p><p>Federico</p><p><br></p><p><br></p><br/><br/> Federico Abascal replied:<br/><p>Dear Konstantin, I have a related question. I have been exporing the original methylation files and was wondering which thresholds does EpiExplorer use for read coverage and percentage of reads with methylation. In UCSC they recommend requiring at least 10 reads and they assign colors depending on what fraction of the reads is found to be methylated.</p><p><br></p><p>Thanks again,</p><p>Federico</p><p><br></p>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/37-would-it-be-possible-to-also-get-the-rat-genome-rn5-availlable/2013-08-31T10:09:55+00:002013-08-31T10:09:55+00:00Would it be possible to also get the rat genome (rn5) availlable? [preguntes] <p>Dear EpiExplorers,</p><p>Would it be possible to also get the rat genome (rn5) availlable?<br></p><br/><br/> Halachev replied:<br/><p>Dear user, </p><p>If you are planning a larger rat project we would certainly consider contributing. If this is the case, please contact our corresponding authors with more details (http://genomebiology.com/2012/13/10/R96). Otherwise, in order to be worth setting things up, we would need serious user interest in this genome that we have not yet observed.</p>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/26-allow-up-to-five-references/2013-08-31T10:05:32+00:002013-08-31T10:05:32+00:00Allow up to five references [idees] Currently the software allows only one reference to be compared to the current set of regions. We suggest to allow up to five references as this will make it more easy to discretize numeric scores and to follow trends. On the other hand 5 is a compromise number as it will still allow to visualize most plots nicely.<br/><br/> Anònim replied:<br/>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/27-human-genome-hg19-support/2013-08-31T10:02:42+00:002013-08-31T10:02:42+00:00Human genome (hg19) support [idees] [completat]<br/><br/> Halachev replied:<br/>Halachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/29-allow-upload-of-gz-files-would-put-less-demand-on-the-client-and-server/2013-08-31T10:00:16+00:002013-08-31T10:00:16+00:00Allow upload of .gz files (would put less demand) on the client and server. [idees] <br/><br/> Anònim replied:<br/>Halachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/32-im-a-new-user-and-when-trying-to-upload-a-set-of-regions-i-got-errno-122-disk-quota-exceeded-im/2013-08-31T10:00:07+00:002013-08-31T10:00:07+00:00I'm a new user, and when trying to upload a set of regions I got "[Errno 122] Disk quota exceeded:". I'm well under the 1,000,000 region limit. Any ideas? [errors] <br/><br/> Anònim replied:<br/><p>It uploaded successfully. Thanks!<br></p>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/47-for-every-view-allow-to-export-the-full-annotated-data-for-every-region/2013-08-31T08:19:17+00:002013-08-31T08:19:17+00:00For every view, allow to export the full annotated data for every region [idees] Currently at every view the user can export the processed table that represents the view data and also the list of current regions. <br><br>It would be useful if he can export the current set of regions with full annotated data from the view for every region<br/><br/> Anònim replied:<br/>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/30-how-to-get-into-the-epiexplorer/2013-08-31T06:59:15+00:002013-08-31T06:59:15+00:00how to get into the Epiexplorer [preguntes] <br/><br/> Halachev replied:<br/><p>You can visit <a href="http://epiexplorer.mpi-inf.mpg.de">http://epiexplorer.mpi-inf.mpg.de</a></p><p><br></p><p>If this does not answer the question, can you please give more details on what do you mean?</p>Anònimtag:epiexplorer.userecho.com,2013-08-31:/communities/1/topics/43-upload-multiple-annotation-datasets/2013-08-31T05:28:50+00:002013-08-31T05:28:50+00:00Upload multiple annotation datasets [idees] <p>Allow uploading multiple annotation datasets (e.g. as BED files) using the same options. This would guarantee that the annotations are comparable, as they all use the same genome version, strand information, etc. and are tested w.r.t. the same default annotations available in <b>EpiExplorer</b>.<br></p><br/><br/> Halachev replied:<br/><p>Can you please specify the data for which chart do you want to have available? </p><p>Every chart has a 'to table' button where the numbers from the chart are shown and exportable. </p><p>Also every chart has a 'to png' button so that you don't need to use printscreen</p>Yassenhttps://epiexplorer.userecho.com/users/5-yassen/topics/tag:epiexplorer.userecho.com,2013-05-15:/communities/1/topics/49-epiexplorer-to-allow-providing-of-tissuecell-lines-for-custom-datasets-and-adapt-its-visualizations/2013-05-15T17:08:13+00:002013-05-15T17:08:13+00:00EpiExplorer to allow providing of tissue/cell lines for custom datasets and adapt its visualizations [idees] When uploading a dataset, the user can provide the tissue/cell line for which the data was computed. <br><br>EpiExplorer can then use the same tissue as default (if available) for its visualizations.<br><p><br></p><br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2013-05-08:/communities/5/topics/18-what-is-an-overlap-criterion/2013-05-08T20:23:53+00:002013-05-08T20:23:53+00:00What is an overlap criterion? [preguntes] <p>An overlap criterion is used to define when is a region from a dataset "overlaps" with a particular annotation. <br></p><br><p>EpiExplorer supports three main overlap criteria: <br></p><ul><li>Any overlap (at least 1bp) <br></li><li>Medium overlap (at least 10%)<br></li><li>Strong overlap (at least 50%)<br></li></ul><p>Selecting an overlap criterion "Strong overlap (at least 50%)" means that in order for a region from the dataset to be considered "overlapping" with a particular annotation, at least 50% of the region need to be covered by the annotation.</p><p><br></p><p>Example: If a dataset contains a region (chr1, 1000,2000) and we are computing with an annotation that is defined in a region (chr1,1850,2050) then the part of the dataset region that is covered by the annotation is (chr1, 1850,2000) which is 150bp. The overlap ratio for the dataset region for this annotation then is 150bp from 1000bp or 15%. This means that if you select a cutoff of 10% this region will be counted, but if you select a cutoff of 50%, it won't. <br></p><p><br></p><p>The choice of the three criteria may seem arbitrary, but the feedback we've had shows that these cover the majority of scenarios. Also they are fixed only for convenience. If needed EpiExplorer allows to customize the criteria by visualizing the distribution of the overlap ratios and filtering by it. This way you can achieve any arbitrary criteria that you prefer. <br></p><br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2013-05-07:/communities/1/topics/48-allow-the-download-of-all-overlap-results/2013-05-07T09:15:07+00:002013-05-07T09:15:07+00:00Allow the download of all overlap results [idees] <p>The server does a great job by calculating the overlaps with ENCODE data and the web interface is adequate for browsing results. However, as soon as one wants to perform some more serious analysis on the overlap results, the web interface becomes a nuisance. <span style=""> It would be very useful if it would be possible to download all the overlap results as a archive of csv files. </span></p><br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2012-10-26:/communities/1/topics/44-i-am-not-been-able-to-save-the-png-clicking-or-write-clicking-on-it-doesnt-allow-me-save-the-png/2012-10-26T08:06:34+00:002012-10-26T08:06:34+00:00I am not been able to save the PNG. Clicking or write clicking on it doesnt allow me save the PNG locally [preguntes] [respost]I am not been able to save the PNG. Clicking or write clicking on it doesnt allow me save the PNG locally<p> </p><br/><br/> Halachev ha canviat a Respost Anònimtag:epiexplorer.userecho.com,2012-09-28:/communities/1/topics/46-support-missing-values-for-scores/2012-09-28T13:21:42+00:002012-09-28T13:21:42+00:00Support missing values for scores [idees] If the score column contains missing values, the corresponding regions can be (or are automatically) filtered out. Missing values are recognized by empty strings, NA, n/a, or something similar.<br><br/><br/> albrecht ha canviat a Yassenhttps://epiexplorer.userecho.com/users/5-yassen/topics/tag:epiexplorer.userecho.com,2012-09-28:/communities/1/topics/35-allow-uploading-sets-of-gene-identifiers/2012-09-28T11:26:55+00:002012-09-28T11:26:55+00:00Allow uploading sets of gene identifiers [idees] <p>Make possible to upload and annotate only a set of gene identifiers<br></p><br/><br/> Halachev replied:<br/><br>Anònimtag:epiexplorer.userecho.com,2012-04-20:/communities/1/topics/24-names-of-regions-in-dna-methylation-broad/2012-04-20T11:51:10+00:002012-04-20T11:51:10+00:00Names of regions in "DNA methylation (BROAD)" [idees] [completat]The names of the region sets in section "DNA methylation (BROAD)" look ugly. It would be nicer if you use space instead of underline (like in all other region set names), and make the capitalization consistent.<br/><br/> Halachev ha canviat a Completat Anònimtag:epiexplorer.userecho.com,2012-04-20:/communities/1/topics/39-rename-reference-dataset-to-shuffle-shuffle-dataset/2012-04-20T11:46:55+00:002012-04-20T11:46:55+00:00Rename reference dataset to shuffle shuffle dataset. [idees] [completat]<br/><br/> Halachev ha canviat a Completat albrechthttps://epiexplorer.userecho.com/users/3-albrecht/topics/tag:epiexplorer.userecho.com,2012-04-11:/communities/1/topics/41-please-allow-per-sequence-in-a-dataset-annotation-instead-of-whole-dataset-annotation/2012-04-11T08:38:47+00:002012-04-11T08:38:47+00:00Please allow per-sequence (in a dataset) annotation instead of whole dataset annotation [idees] The current annotation format shows percentage / information for the whole dataset, it will be useful to have the annotation for each sequence in the dataset independently, Thanks<br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2012-03-01:/communities/1/topics/36-report-the-genome-coverage-of-every-feature-and-of-the-current-set-of-regions/2012-03-01T06:43:25+00:002012-03-01T06:43:25+00:00Report the genome coverage of every feature and of the current set of regions [idees] [started]<br/><br/> Halachev ha canviat a Started Anònimtag:epiexplorer.userecho.com,2012-02-10:/communities/1/topics/38-show-more-information-about-the-used-annotations/2012-02-10T07:51:11+00:002012-02-10T07:51:11+00:00Show more information about the used annotations [idees] [started]Show source of the data, short description of the data, date on which it was obtained, method via which it was processed etc<br><br/><br/> Halachev ha canviat a Started Halachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2012-02-10:/communities/1/topics/20-mouse-genome-mm9-support/2012-02-10T07:46:23+00:002012-02-10T07:46:23+00:00Mouse genome (mm9) support [idees] [completat]<br/><br/> Halachev ha canviat a Completat Halachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2012-01-27:/communities/1/topics/22-user-upload-their-own-annotation-data-sets/2012-01-27T09:22:09+00:002012-01-27T09:22:09+00:00User upload their own annotation data sets. [idees] Users to be able to upload not only custom BED files as annotation but also DNA methylation data, histone peaks and others<br><br/><br/>Suggerit per: albrechtalbrechthttps://epiexplorer.userecho.com/users/3-albrecht/topics/tag:epiexplorer.userecho.com,2012-01-24:/communities/1/topics/34-api-to-access-the-data/2012-01-24T13:59:04+00:002012-01-24T13:59:04+00:00API to access the data. [idees] <br/><br/> albrecht replied:<br/>An API to access the EpiExplorer data, allowing the extensions. albrechthttps://epiexplorer.userecho.com/users/3-albrecht/topics/tag:epiexplorer.userecho.com,2012-01-24:/communities/1/topics/40-dynamically-update-a-visualization-based-on-the-slider-movement/2012-01-24T13:21:51+00:002012-01-24T13:21:51+00:00Dynamically update a visualization based on the slider movement [idees] Currently every slider on the left side is couple with a visualization on the right. There is interest if the slider can be reached independently of the visualization, for example filter by length while looking at the summary visualization. Then the goal will be to dynamically show the changes(maybe similar to comparison mode, in gray the current numbers in orange the numbers if the refinment was selected).<br><br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2011-12-14:/communities/1/topics/19-allow-uploading-to-use-as-basis-default-or-custom-already-processed-attributes/2011-12-14T09:39:17+00:002011-12-14T09:39:17+00:00Allow uploading to use as basis default or custom already processed attributes [idees] On the upload page currently it is allowed a new dataset to be specified either by pasting the bed data int he text area or uploading it in the file field. Add a third option to use as region set one of the default (or loaded custom ) datasets.<br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2011-11-25:/communities/1/topics/28-add-filtering-of-omim-terms-based-on-the-number-of-genes-as-for-the-go-terms/2011-11-25T05:03:31+00:002011-11-25T05:03:31+00:00Add filtering of OMIM terms based on the number of genes, as for the GO terms [idees] <br><br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2011-08-08:/communities/1/topics/42-history-of-the-last-several-visualizations/2011-08-08T07:14:43+00:002011-08-08T07:14:43+00:00History of the last several visualizations [idees] <br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2011-08-08:/communities/1/topics/45-help-bubbles/2011-08-08T04:47:18+00:002011-08-08T04:47:18+00:00Help bubbles [idees] <p>Allow more help bubbles? <br></p><p>For datasets information, tissues, plots, computations and others<br></p><p><br></p><p>One of those<br></p><p><br></p><p><a href="http://craigsworks.com/projects/qtip/">http://craigsworks.com/projects/qtip/</a></p><p><br></p><p><a href="http://craigsworks.com/projects/qtip2">http://craigsworks.com/projects/qtip2</a><br></p><p><br></p><p><a href="http://www.vegabit.com/jquery_bubble_popup_v2/">http://www.vegabit.com/jquery_bubble_popup_v2/</a> <br></p><br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2011-07-08:/communities/1/topics/50-add-a-profile-plot-similar-to-the-neighborhood-plots/2011-07-08T06:24:51+00:002011-07-08T06:24:51+00:00Add a profile plot similar to the neighborhood plots [idees] Add a profile how often certain positions inside the regions, such as the start, the middle and the end overlap with a certain property. <br><br>For example, a profile plot showing 5,10,15,11,6 for the overlap of set of regions with CGIs will show that the 5'end overlaps in 5%, the 1/4 point overlaps in 10%, the middle point overlaps in 15% etc and would be indicative that the middle of the regions tend to be more overlapping with CGIs than the ends.<br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/tag:epiexplorer.userecho.com,2011-05-23:/communities/1/topics/21-custom-dna-sequence-patterns/2011-05-23T02:24:01+00:002011-05-23T02:24:01+00:00Custom DNA sequence patterns [idees] Currently if DNA sequence is selected only the preselected basic sequence patterns are computed. Please, allow the user to specify custom DNA sequence patterns<br/><br/>Suggerit per: AnònimAnònimtag:epiexplorer.userecho.com,2011-05-10:/communities/1/topics/23-search-for-similar-regions/2011-05-10T02:56:40+00:002011-05-10T02:56:40+00:00Search for similar regions [idees] Find all genomic locations that are similar to a given one w.r.t. certain criteria. <br/><br/>Suggerit per: HalachevHalachevhttps://epiexplorer.userecho.com/users/1-halachev/topics/