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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.

Thanks in advance.

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    $\begingroup$ This might be better suited to [Academia] where people from more fields could know about a place for such things. $\endgroup$ – llrs Sep 6 '18 at 7:19
  • $\begingroup$ @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. $\endgroup$ – Scientist Sep 6 '18 at 13:38
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You may try Code Ocean. Currently, it is not that easy to use IMHO, but one of their tech leads promises to substantially improve it towards the year end.

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  • $\begingroup$ 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. $\endgroup$ – Scientist Sep 6 '18 at 15:41
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I have seen some (1 or more) articles with interactive data displays in the F1000Research journal I don't know recall now if they had interactive tables or plots but they used plotly for sure.

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  • $\begingroup$ 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. $\endgroup$ – Scientist Sep 6 '18 at 15:43
  • $\begingroup$ Yes, I realized later that your data seems "huge" so a publisher doesn't seem a good choice to store the data $\endgroup$ – llrs Sep 6 '18 at 15:47
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    $\begingroup$ 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. $\endgroup$ – Scientist Sep 6 '18 at 16:17
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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. 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).

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    $\begingroup$ If you have problems scaling shiny apps you might find this post interesting. $\endgroup$ – llrs Sep 6 '18 at 7:18
  • $\begingroup$ 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 !.. $\endgroup$ – Scientist Oct 22 '18 at 14:22

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