Answers.Body: <p>You may try <a href="https://codeocean.com" rel="nofollow noreferrer">Code Ocean</a>. Currently, it is not that easy to use IMHO, but one of their tech leads promises to substantially improve it towards the year end.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T15:41:25.260Z
Answers.Text: I have just looked into Code Ocean as you suggested, and though it looks promising it is indeed not very user-friendly at the moment... Plus, looks like one needs a subscription to run interactive content.
Answers.UserDisplayName: Scientist
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T14:18:11.047Z
Answers.LastActivityDate: 2018-09-06T14:18:11.047Z
Answers.UserDisplayName: user172818
Answers.Body: <p>I have seen some (1 or more) articles with interactive data displays in the <a href="https://f1000research.com/articles/" rel="nofollow noreferrer">F1000Research journal</a> I don't know recall now if they had interactive tables or plots but they used plotly for sure.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T15:43:15.290Z
Answers.Text: Yes, I heard that F1000 encourages plotly content. I have just sent them an email. However that would be a journal option for a final publication (if I can pay their fees). Ideally, right now I'd greatly benefit from an external repository that could also be used with a preprint server like Bioarxiv. Unfortunately bioarxiv seems to only take .pdf output.
Answers.UserDisplayName: Scientist
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T15:47:01.283Z
Answers.Text: Yes, I realized later that your data seems "huge" so a publisher doesn't seem a good choice to store the data
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T16:17:11.307Z
Answers.Text: Mind that by "huge" we mean a table is very large in numbers of rows. In reality the actual data behind the table are .txt files adding up to less than 20 Mb. I could in principle publish such table as a .pdf file, however nobody would like it and read it.
Answers.UserDisplayName: Scientist
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T07:24:40.017Z
Answers.LastActivityDate: 2018-09-06T07:24:40.017Z
Answers.UserDisplayName: llrs
Answers.Body: <p>The example looks a lot like a shiny application. Your best bet then is one of the following:</p>
  
  <ul>
  <li>Ask your IT department to setup a shiny server for you. They can use the free version.</li>
  <li>Post your shiny app on <a href="https://shiny.rstudio.com/deploy/" rel="nofollow noreferrer">shinyapps.io</a>. Depending on how popular the page becomes, you might have to pay for an account.</li>
  </ul>
  
  <p>The free version of shiny works for most cases (it's what we use), the only problem with it is that it doesn't scale (but if you care about that then you need to either pay for hosting on a pro server or buy a shiny pro license).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-22T14:22:16.587Z
Answers.Text: Only now I see the issue you mention about popularity. On a free account I only get 24 mins of server availability per month. Given my scope of use, this is way too short !..
Answers.UserDisplayName: Scientist
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-06T07:18:25.917Z
Answers.Text: If you have problems scaling shiny apps you might find [this](https://blog.rstudio.com/2018/06/26/shiny-1-1-0/) post interesting.
Answers.UserDisplayName: llrs
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Answers.CreationDate: 2018-09-06T07:12:31.450Z
Answers.LastActivityDate: 2018-09-06T07:12:31.450Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am not sure whether this is the best SE community for this question. </p>
  
  <p>I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables that can be filtered &amp; searched for specific entries. </p>
  
  <p>I would like to publish such a table as supplementary to a paper (e.g. preprint version) however usually data repositories allow for uploading files and text. </p>
  
  <p>Would anyone here know an official data repository with a format such that would enable publishing online an interactive table? </p>
  
  <p>A good example of such a table is given <a href="http://butterlab.imb-mainz.de/flydev/?data=embryogenesis" rel="nofollow noreferrer">here</a>.</p>
  
  <p>Thanks in advance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-06T07:19:25.270Z
Comments.Text: This might be better suited to [Academia] where people from more fields could know about a place for such things.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-06T13:38:34.763Z
Comments.Text: @Llopis I will also ask there, thanks! My guess is that they'll think it is mostly technical and redirect me elsewhere. I think it is in fact a quite specific question on a situation not many have faced yet.
Comments.UserDisplayName: Scientist
Tags: <r><public-databases><public-dataset>
Title: Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?
ThreadText: # Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?
  
  (Asked by: username_0 on 2018-09-05)
  
  I am not sure whether this is the best SE community for this question.
  
  I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables that can be filtered & searched for specific entries.
  
  I would like to publish such a table as supplementary to a paper (e.g. preprint version) however usually data repositories allow for uploading files and text.
  
  Would anyone here know an official data repository with a format such that would enable publishing online an interactive table?
  
  A good example of such a table is given [here](http://butterlab.imb-mainz.de/flydev/?data=embryogenesis).
  
  Thanks in advance.
  
  **Tags:** r, public-databases, public-dataset
  
  > **Comments:**
  > **username_1**: This might be better suited to [Academia] where people from more fields could know about a place for such things.  
  > **username_0**: @Llopis I will also ask there, thanks! My guess is that they'll think it is mostly technical and redirect me elsewhere. I think it is in fact a quite specific question on a situation not many have faced yet.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2018-09-06. Score: 3
  
  You may try [Code Ocean](https://codeocean.com). Currently, it is not that easy to use IMHO, but one of their tech leads promises to substantially improve it towards the year end.
  
  > **Comments:**
  > **username_0**: I have just looked into Code Ocean as you suggested, and though it looks promising it is indeed not very user-friendly at the moment... Plus, looks like one needs a subscription to run interactive content.  
  
  ---
  
  ### Answer by username_1 on 2018-09-06. Score: 2
  
  I have seen some (1 or more) articles with interactive data displays in the [F1000Research journal](https://f1000research.com/articles/) I don't know recall now if they had interactive tables or plots but they used plotly for sure.
  
  > **Comments:**
  > **username_0**: Yes, I heard that F1000 encourages plotly content. I have just sent them an email. However that would be a journal option for a final publication (if I can pay their fees). Ideally, right now I'd greatly benefit from an external repository that could also be used with a preprint server like Bioarxiv. Unfortunately bioarxiv seems to only take .pdf output.  
  > **username_1**: Yes, I realized later that your data seems "huge" so a publisher doesn't seem a good choice to store the data  
  > **username_0**: Mind that by "huge" we mean a table is very large in numbers of rows. In reality the actual data behind the table are .txt files adding up to less than 20 Mb. I could in principle publish such table as a .pdf file, however nobody would like it and read it.  
  
  ---
  
  ### Answer by username_3 on 2018-09-06. Score: 1
  
  The example looks a lot like a shiny application. Your best bet then is one of the following:
  
  * Ask your IT department to setup a shiny server for you. They can use the free version.
  * Post your shiny app on [shinyapps.io](https://shiny.rstudio.com/deploy/). Depending on how popular the page becomes, you might have to pay for an account.
  
  The free version of shiny works for most cases (it's what we use), the only problem with it is that it doesn't scale (but if you care about that then you need to either pay for hosting on a pro server or buy a shiny pro license).
  
  > **Comments:**
  > **username_1**: If you have problems scaling shiny apps you might find [this](https://blog.rstudio.com/2018/06/26/shiny-1-1-0/) post interesting.  
  > **username_0**: Only now I see the issue you mention about popularity. On a free account I only get 24 mins of server availability per month. Given my scope of use, this is way too short !..  
  
  ---
  
  