#shiny

2021-10-07

Shila Ghazanfar (13:16:34): > @Shila Ghazanfar has joined the channel

2021-10-16

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2022-01-03

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2022-08-11

Shila Ghazanfar (04:38:07): > set the channel description: Discussion around use of Shiny within Bioconductor packages!

Kevin Rue-Albrecht (04:39:04): > @Kevin Rue-Albrecht has joined the channel

Vince Carey (07:05:46): > @Vince Carey has joined the channel

Vince Carey (07:09:50): > How do we rank approaches to interaction with genomic data? The UCSC genome browser is well-known and widely used, and the basic points of entry are gene or position/region and “track”. IGV and Jbrowse have similar roles.

Vince Carey (07:14:51): > To help investigators think about how to connect their eQTL and GWAS results to gene models I madehttps://vjcitn.shinyapps.io/tnt4dn8/which is based on TnT and is very slow to load. Note that there is no “y axis” for the data tracks; the TnT folks were queried on this. Highly interactive “track layering” seems very desirable, but what’s the best way forward when starting with GRanges as tracks?

Vince Carey (07:20:34): > Examples herehttps://github.com/igvteam/igv.js#igvjsseem very worthwhile; should we be able to “plug” igv into shiny without too much effort? I don’t know where to begin.

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Marcel Ramos Pérez (09:48:33): > How abouttrackViewer?

Kevin Rue-Albrecht (10:35:27): > igv.js as a widget sounds fun > As a heads up, now that I’ve startedhttps://github.com/kevinrue/iSEEExperimentHubI’m considering supporting GRanges and other objects that can be embedded (not coerced) into SummarizedExperiment objects

Kevin Rue-Albrecht (10:36:47): > But the nature of iSEE means that we’ll always be limited to objects where rows are features and columns are samples. Which is why genomic tracks has always been an unsolved headache in iSEE so far

Kevin Rue-Albrecht (11:33:07): > That was to say that having nowGRangesreadily available through theExperimentHubis now a good motivation to toy with them iniSEEapps, which obviously includes displaying them on genomic tracks. The tough part being the handling of selections through shiny brushes, which need to convert coordinates of selection in the app to indices of items in theSummarizedExperimentobject

Marcel Ramos Pérez (12:55:21) (in thread): > May be of interest :https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/ - Attachment (NCBI Insights): Introducing the Comparative Genome Viewer (CGV) beta release - NCBI Insights > NLM’s NCBI is introducing the Comparative Genome Viewer (CGV), an easy-to-use visualization tool that helps you quickly compare eukaryotic genome assemblies and easily identify genomic changes that may be significant to biology and evolution. With the new CGV you can view and compare the alignment between two assemblies to see differences in genomic sequence and … Continue reading Introducing the Comparative Genome Viewer (CGV) beta release →

Jared Andrews (18:27:06): > @Jared Andrews has joined the channel

2022-08-12

Jared Andrews (14:38:47): > re: IGV in shiny, seehttps://www.bioconductor.org/packages/release/bioc/html/igvR.htmlandhttps://github.com/paul-shannon/igvShiny. Paul Shannon, the author of these, gave a brief talk on them at Bioc2022, but there were significant technical issue so his slides weren’t displayed.

2022-08-15

Federico Marini (10:00:53): > @Federico Marini has joined the channel

2022-08-26

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2022-08-31

Shila Ghazanfar (10:30:19): > hi all, i wanted to share this thread into the shiny channel as it’s so rich with ideas and discussion around shiny and bioconductor. thanks kevin and jared for your thoughts - Attachment: Attachment > I suppose I will apply and do my best. Was hoping someone familiar with shiny would warn me of common pitfalls before I submit.

Shila Ghazanfar (10:32:25): > and this follow-on thread which had some nice ideas, e.g.InteractiveVisualizationas an additional BiocViews topic.. would love to discuss more on ideas/challenges/thoughts - Attachment: Attachment > thanks for this thread @Jared Andrewsand @Kevin Rue-Albrecht, i read with a lot of interest! I’m in general interested in how many packages across Bioconductor are including shiny app loaders as part of the package and what (if any) special considerations needed for such packages. I created a #shiny channel with this in mind way back but no activity as yet, this channel could be a place to discuss such topics? just a thought :slightly_smiling_face: pinging @Federico Marini too :)

Jared Andrews (12:11:09): > Honestly, just go look at iSEE if you’re doing anything with Shiny. While it’s huge and complex, it does a bunch of stuff I wasn’t aware was even possible in terms of how to break up and organize an app while gracefully handling reactives/observers.

Jared Andrews (12:13:10): > There are frustratingly few resources as to how best package complex apps in the official docs, particularly in terms of creating and handling reactives outside the typicalapp.Rorui.randserver.rsetups.

Shila Ghazanfar (19:49:27): > thanks for this jared! do you think the Mastering Shiny textbook (https://mastering-shiny.org/) is helpful, or are the aspects that are more specific to bioconductor-y analysis not captured? - Attachment (mastering-shiny.org): Welcome | Mastering Shiny > A book created with bookdown.

2022-09-01

Kevin Rue-Albrecht (07:24:32) (in thread): > If I’m being honest, I don’t remember ever reading that book myself. I can see that the first commit for that book was 9 July 2016 (https://github.com/hadley/mastering-shiny/commit/1a73f4af6211df45ec03519ef16a71975e2f96aa). A Google search seems to indicate that shiny itself was released in 2012 (https://www.r-bloggers.com/2012/11/rstudio-releases-shiny/). > > I can’t remember when I started using shiny myself, but I think I started from the basic examples in the man pages of the shiny package, and built up my own experience from there. > > I can see that the book starts with a chapter “your first shiny app”, which is effectively the same thing. Plus, the quality of Hadley’s books is such that I strongly encourage new (and experienced) shiny app developers to seriously consider reading that book (either in order or skipping bits when they are confident to do so). > > During the development of iSEE, I learned a lot from my co-developers, each of us having brought our own personal experience of shiny from our own, typically smaller apps, that we had developed individually. > To this date, we still frequently discuss and collectively make up and agree on best practice when updating, fixing, or adding new code - Attachment (R-bloggers): RStudio releases Shiny | R-bloggers > RStudio has released a new package for R. Shiny allows R developers to build simple interactive Web-based interfaces for R scripts, using only R code (no JavaScript development required!). You can see some examples of Shiny in action in this blog post, and there are more details about Shiny’s capabilities in this tutorial. Shiny was first announced to beta testers back in July at the JSM 2012 conference. RStudio’s Joe Cheng gave several demonstrations of Shiny in action to the audience, which I captured in the video below: Shiny has evolved in the four months since then, and I look…

Jared Andrews (17:42:15) (in thread): > Yeah, I mean that book is definitely helpful, I referenced it pretty heavily to wrap my head around the reactivity concepts when I was starting out. > > I think once you start getting to relatively complex apps, it just helps to look at some really well-made examples where the structure and organization of the app clearly had a lot of thought and effort put into them.

2022-09-15

Shila Ghazanfar (06:20:15): > hi everyone! at EuroBioc2022 i was thinking of proposing a BOF session around bioc users and developers use of interactive apps, with the goal to identify gaps, what available resources needs to be promoted more, and any ideas to then take forward to community etc.. just going to start a doc here and would love any input:pray::))https://docs.google.com/document/d/1b_hSBAuPA4kjfK1ZMwe4Sdfk-iB3-8llb0Z_8GkO7RQ/edit

Kevin Rue-Albrecht (07:30:47) (in thread): > now i’m even more sad of missing the conference:wink:

Shila Ghazanfar (07:51:47) (in thread): > would love to have you involved beyond the BOF of course!! sorry for the fomo:slightly_smiling_face:

Kevin Rue-Albrecht (07:52:56) (in thread): > just teasing:wink:i look forward to hearing the outputs of the BOF

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2022-09-16

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Lisa Breckels (03:45:43) (in thread): > Hi Shila, I have to leave early this morning so won’t make the birds of a feather sadly. Very interested to hear the output from this session though:slightly_smiling_face:I am author ofpRolocGUIhttps://bioconductor.org/packages/release/bioc/html/pRolocGUI.htmland maintain many apps for our group account atshinyapps.iowhich we disseminate with publications that stem from our Bioc package. > > Biggest issues I have are related to speed and debugging! I’ll have a read through the Google doc.

Kevin Rue-Albrecht (04:03:14) (in thread): > We’ve got a candidate visiting the lab in oxford this morning, i’ll be busy from 12pm your time, i might be able to join the bof at 11pm (is shiny then or later?) your time if someone wants to call me on slack or whatever. Don’t mind me too much then, in case soething coems up on my side

Shila Ghazanfar (04:22:50) (in thread): > thanks so much lisa@Lisa Breckels!! that’s wonderful and i’m copying your message into the document:slightly_smiling_face:

Shila Ghazanfar (04:23:29) (in thread): > thanks kevin will update with updated schedule :)

Shila Ghazanfar (04:38:30) (in thread): > we’re going to do a quick survey at 11am whether the BoF sessions will be parallel or consecutive, so will be able to update you as it happens:slightly_smiling_face:

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Kevin Rue-Albrecht (07:08:38) (in thread): > Really impressed by the amount of feedback and ideas in the GDoc!

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Paul Shannon (12:33:32): > Shiny has many virtues. One obstacle I encountered in building structured applications, is that shiny widget state can be hard to track. RStudio introduced modules to help with this, but this solution, in my eyes, introduces more complexity and tricks than benefits. For instance, a module name is automatically prepended to messages sent to Javascript. I prefer explicit coding… > > So I picked up on a proposal and demo whose source I now forget, and now often useR6classes, one per widget, each with their own state.

Paul Shannon (12:35:16): > If this interests you, check out a minimal and very simple example:https://github.com/PriceLab/BioShiny/tree/master/MsgBoxWidget - File (PNG): image.png

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Kevin Rue-Albrecht (14:05:01): > Nice approach@Paul ShannonOn a separate note, I’ve updated the shiny page of the contribution guidehttp://contributions.bioconductor.org/shiny.htmlwith an overdue transfer of comments in that threadhttps://community-bioc.slack.com/archives/C029XJX3A4F/p1660134829013599I am intentionally flirting with over-prescriptive guidelines, if only to establish a baseline to foster discussion and refinements - Attachment (contributions.bioconductor.org): Chapter 17 Shiny apps | Bioconductor Packages: Development, Maintenance, and Peer Review > Shiny apps can be submitted to Bioconductor as software packages. 17.1 Code organisation Shiny apps are divided into two parts: User interface (UI) Server Shiny apps submitted to Bioconductor… - Attachment: Attachment > I suppose I will apply and do my best. Was hoping someone familiar with shiny would warn me of common pitfalls before I submit.

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Paul Shannon (19:22:22) (in thread): > Hi Vince, By “plug” I imagine you mean something other that what we do in igvShiny. Could you explain? I mighthave some ideas.

2022-09-17

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Vince Carey (12:05:15) (in thread): > i think at that time i did not know about igvShiny?

Vince Carey (12:09:14): > has anyone used shinytest with a bioc-related shiny app? i saw no reference to it in iSEE; the test suite for iSEE is substantial. would there be gains from using shinytest?

Kevin Rue-Albrecht (12:23:45) (in thread): > Haven’t used it yet. Can’t remember looking into it, mostly because I’ve always been happy with the coverage achieved using testthat

2022-09-18

Paul Shannon (00:56:45) (in thread): > I tried it, but it has been a couple of years ago now. With shinytest, you establish a reference via screen captures at specified points in the shiny app’s execution. Then the subsequent execution test compares a new screen capture to that reference, pixel by pixel. We found that this is hardware display specific - that a reference created on one display failed against a subsequent test on another display, even when the display resolution was the same. I cannot remember the details, but I think we also sometimes had trouble comparing reference and test on the same monitor. > > Perhaps it would be better to test at a level higher than display pixel equality. We had some luck with, but did not follow through on, a homegrown testing scheme based on events. I could elaborate if there is any interest.

Nils Eling (10:46:01) (in thread): > I was using shinytest for testing cytomapper for a while and in general it kind of worked. Instead of testing images of the GUI (in PNG format) I only tested changes to a JSON representation of the app. I nearly got to the point where it allowed testing via CI but as soon as the version of a dependency changes the tests fail. There is still an open issue that hasn’t been addressed yet to allow testing via an automated build (https://github.com/rstudio/shinytest/issues/243).

2022-09-19

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2022-09-20

Federico Marini (08:11:40) (in thread): > IIRC they did a major revamp to shinytest recently, and I think they presented something at the recent rstudio::conf. I can check it up

Federico Marini (08:12:46) (in thread): > So, indeed there ishttps://rstudio.github.io/shinytest/but alsohttps://rstudio.github.io/shinytest2/ - Attachment (rstudio.github.io): Test Shiny Apps > For automated testing of Shiny applications, using a headless browser, driven through WebDriver. - Attachment (rstudio.github.io): Testing for Shiny Applications > Automated unit testing of Shiny applications through a headless Chromium browser.

Federico Marini (08:12:57) (in thread): > the second one also being on CRAN, but just.. recent

Federico Marini (08:13:22) (in thread): > and in “lifecycle: experimental”

Federico Marini (08:14:22) (in thread): > Yet: here’s a presentation of it at the conf –>https://www.youtube.com/watch?v=EOVPBN5o8F8 - Attachment (YouTube): Barret Schloerke: {shinytest2} Testing Shiny with {testthat}

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Vince Carey (14:27:33): > Thishttps://github.com/ndcn/omicseris mentioned at CZI open science meeting, referencing golem.https://engineering-shiny.org/golem.html - Attachment (engineering-shiny.org): Chapter 4 Introduction to {golem} | Engineering Production-Grade Shiny Apps > img.left { float: left; margin-right: 1em; } The {golem} (Fay et al. 2021) package is a framework for building production-grade {shiny} applications. Many of the patterns and methodologies…

2022-12-01

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2022-12-13

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2022-12-15

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2022-12-23

Vince Carey (06:59:49): > alpha testing?https://shiny.rstudio.com/py/docs/get-started.html

2022-12-30

Federico Marini (13:21:16): > not really, it got announced at the rstudio conf recently

Federico Marini (13:21:30): > so, yes, might be lacking quite some features, but it got out “officially”

Jared Andrews (14:39:58): > they still say it may having breaking changes

Jared Andrews (14:40:31): > I don’t know if that’s true or not, but I’ve held off doing anything with it due to that for now

2023-01-12

Janani Ravi (01:34:30) (in thread): > Kevin, are you one of thepoint of contact folks for this—BioC shiny app packages?

Janani Ravi (01:39:03) (in thread): > What’s the typical data/size/storage cap on experimenthub/isee, especially the former?Do you happen to know this off the top of your head?

Kevin Rue-Albrecht (04:03:35) (in thread): > If I understand you well, then I’ve had that conversation with CAB and some core members, and my current understanding is that no one really knows the size of each individual data set in the Ehub

Kevin Rue-Albrecht (04:07:56) (in thread): > Depends on the nature of your question. I’ve set up the repository for the contributions guidelines and wrote some of the contents myself, but some questions require feedback form bioc core:wink:

Janani Ravi (10:27:16) (in thread): > I wanted to explore the fit of our shiny app to the bioc package option.Let me look into this a bit more carefully and ping you again.

Kevin Rue-Albrecht (10:29:06) (in thread): > OK, no problem. Ask away, and if I can help I’ll reply, otherwise we can get others involved. My main mission is that the guidelines grow in usefulness and clarity, I don’t mind who write them:slightly_smiling_face:

Janani Ravi (10:29:19) (in thread): > Hmm, so 100-150gb is a possibility then?@Lori Shepherdwould you have some insight? > > I’m looking for a good avenue to release data packages.Sean suggested ehub.Hence the question.I can furnish further details in case that would be helpful.Thanks, both!

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2023-03-07

Vince Carey (06:30:33): > Well, I haven’t tried golem yet, but I did use shinytest::recordTest on a new app. What I find is that the testing procedure produces PNG files as snapshots of app appearance. If you do fairly rigorous testing, you will have quite a few MB of PNG in the resulting test folder. One would quickly exceed the 5MB package size limit if doing this in a Bioconductor package. I don’t know how to address this at this time.

Vince Carey (06:31:58): > I would comment also that I find shinyMobile package fairly intriguing. It would be nice to be able to use an app on the phone or tablet to get information about certain aspects of the project.

2023-03-08

Federico Marini (08:29:44): > I never used shinyTest per se, but I knew it had this “drawback”. > In iSEE we have implemented a different kind of tests, “for the app” but not in that framework. > > And from a recent posit/rstudio conf, I seem to recall they have a younger brother for that package, and that might be the new way to go with this:https://github.com/rstudio/shinytest2/

Vince Carey (12:29:18): > Thanks@Federico Marini!

2023-03-16

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2023-03-28

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2023-04-21

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2023-04-23

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2023-04-24

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2023-04-26

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2023-05-16

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2023-05-17

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2023-05-25

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2023-05-31

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2023-06-07

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2023-06-16

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2023-06-20

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2023-07-12

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2023-07-28

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2023-08-02

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2023-08-04

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2023-08-07

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2023-09-07

Ismael Rodriguez (05:02:15): > Hello:wave:I’ve made a list of really cool Shiny apps for Pharma and Biotech:https://go.appsilon.com/pharma-apps(also see the doc attached). > > We’ve recently launched these two at Appsilon: > FDA-Pilot-App:https://go.appsilon.com/fda-clinical-trial …Drug Interactions App:https://go.appsilon.com/fReach out for any questions! - Attachment (appsilon.com): Advancing FDA Clinical Trial Submissions with R: Reproducing the R Submissions Pilot 2 Shiny App Using Rhino - R programming > Discover how to submit a Shiny app through the FDA e-CTD with Rhino. Optimize efficiency and compliance in the drug development process with R programming. - File (PDF): Post_LS_In_compressed (1) (3).pdf

Vince Carey (05:22:05) (in thread): > Can this be addressed? > > Firefox detected a potential security threat and did not continue to app.playground.bigomics.ch. If you visit this site, attackers could try to steal information like your passwords, emails, or credit card details. >

Ismael Rodriguez (05:27:05) (in thread): > Thanks for letting me know, we’ll remove that link (which was given to us by BigOmics).

2023-09-14

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2023-09-20

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2023-09-21

Federico Marini (10:23:48): > Meanwhile, in dreamland…https://x.com/pawel_appsilon/status/1704616436789076380?s=20 - Attachment (X (formerly Twitter)): Paweł Przytuła on X > This is huge! @jcheng announced Shinylive for R at #positconf2023 :fire: > > Now you can: > > 1. Convert Shiny to static HTML/CSS/JS/wasm > 2. Write Shiny apps directly in a browser > 3. Embed Shiny as Quarto code chunks in other webapps > > #rshiny #rstats #positconf

Jared Andrews (10:28:10): > Finally, been waiting for that for a while. Toyed with it in python, but I was rather unwilling to convert everything over.

Jared Andrews (10:31:44): > Also Github copilot integration in RStudio.

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Kevin Stachelek (14:53:14) (in thread): > Would shinylive enable wider sharing of interactive analyses given the limitations of hosting somewhat large datasets and the heavy dependencies of most single cell packages? What do you think is the most robust way to share shiny based single cell analysis tools with wetlab scientists? I currently use open-source shiny server on a small intranet ubuntu webserver that houses our datasets. Are institutional tools like cellxgene etc. the way of the future? I’m typically a user/assembler of bioconductor tools so appreciate the views of developers here.

2023-09-24

Federico Marini (15:46:39) (in thread): > likely not for the more complex apps. But I would like to see it happen, for sure

2023-10-18

Ismael Rodriguez (03:13:34): > Hello everyone:alembic:, for those working in R for regulatory submissions, there is a new blog on the pharmaverse talking about thesuccessful review of the Shiny app submitted to the FDA:https://pharmaverse.github.io/blog/posts/2023-08-14_rhino_submission_2/rhino_submission[…]utm_medium=social&utm_source=linkedin&utm_campaign=articleThis is great for Shiny apps:tada: - Attachment (pharmaverse.github.io): Pharmaverse Blog - Reproducing the R Submissions Pilot 2 Shiny Application using Rhino

2023-11-09

Kevin Rue-Albrecht (09:22:04): > Spotted this article.https://www.r-bloggers.com/2023/11/r-shiny-modules-how-to-create-your-first-r-shiny-mo[…]medium=email&utm_campaign=R-bloggers-daily&utm_content=HTMLHaven’t read it, but I’ve heard a lot of good about shiny modules

Marcel Ramos Pérez (09:26:10) (in thread): > Nice, the original link shows you the images :https://appsilon.com/r-shiny-modules/

2024-02-13

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2024-03-24

Louis Le Nézet (13:16:15): > Hi, > I’m writing a Shiny app for the “Pedixplorer” package. > The aim is to allow easy exploration of huge pedigree in a graphic interface. > I’ve read thedocumentationbut some things are still obscure for me. > > Would their be somewhere a nice developped shiny app in Bioconductor that I could take inspiration from ?

Marcel Ramos Pérez (22:39:31): > Hi Louis, I usually refer to the shiny app gallery for some exampleshttps://shiny.posit.co/r/gallery/but we do have a shiny apps category inbiocViewsthat you can also browse (hopefully, you will find some related shiny apps)https://www.bioconductor.org/packages/release/BiocViews.html#___ShinyApps

2024-03-25

Jared Andrews (08:40:30): > Also take a look at geneTonic, iSEE, and my own CRISPRball for some other examples

Vince Carey (09:32:35): > in case you have to handle files, I foundhttps://github.com/thomasp85/shinyFilesilluminating

2024-04-28

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2024-06-05

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2024-07-05

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2024-07-11

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2024-07-12

Hans-Rudolf Hotz (01:51:22): > https://galaxyproject.org/news/2024-07-26-shiny-phyloseq-on-eu/ - Attachment (galaxyproject.org): Shiny phyloseq interactive tool available on usegalaxy.eu - practical > We are thrilled to announce, that thanks to the help of the Bioconductor community, we could deploy the Shiny phyloseq App as an interactive tool (IT) on usegalaxy.eu

Maria Doyle (04:34:39) (in thread): > Hi@Susan Holmes, I thought you might be interested in this, in case you don’t already know. It’s a Shiny app version of your phyloseq tool available in Galaxy EU.

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2024-07-19

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2024-07-23

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2024-07-25

Louis Le Nézet (10:15:05): > Hi everyone, > I’m building an app for the Pedixplorer package and in the BioConductor guidelines it is said to > > Place internal functions that create observers – e.g.,shiny::observeEvent()– in files namedobservers_*.R. Do this both for observers reacting to the Shiny serverinputobject, and reactive values stored in lists of reactive values (e.g.,shiny::reactiveValues()). > I would like to usereactiveValuesto store parameters selected by the user. > Could anyone provide an example of how such a file might be structured? > Additionally, if you know of any packages that demonstrate good practices in this area, I would appreciate your recommendations. > Thanks a lot and have a great summer !

Jared Andrews (10:22:03): > Hey Louis, you can see an example of how I handled this here:https://github.com/j-andrews7/CRISPRball/blob/devel/R/CRISPRball.RIn short, I initialize areactiveValueslist (robjects) that I pass along to functions that create the observers (which you can see in the variousobservers_*.Rfiles).

Jared Andrews (10:22:56): > I think I looked at iSEE as my original example for doing this.

Kevin Rue-Albrecht (10:31:05): > @Louis Le NézetNote that the current guidelines are somewhat iSEE-centric and open to feedback and suggestions. > For instance, a few months ago there was a discussion of Shiny modules, which I’ve personally never used, so I cannot reasonably propose any guideline for their usage in Bioconductor. > Like most of Bioconductor, these guidelines are driven by the experience and expertise of the community, and shouldn’t be seen as fixed forever:slightly_smiling_face:

Louis Le Nézet (10:32:19): > Thanks I will try to make it work for the EuroBioc2024:grin:

Jared Andrews (10:36:35): > FWIW, I’ve been toying with a package of modules lately (still early:https://github.com/j-andrews7/dittoVizModules) and have some thoughts in terms of their basic organization and usage.

Jared Andrews (10:37:24): > As I get into more complex cases, I will try to write up my thoughts more coherently for discussion.

2024-07-26

Susan Holmes (08:36:04) (in thread): > Thanks Maria, We had originally had a shiny-phyloseq that was actually presented at Bioc 10 years ago in Boston. This is an update because shiny has been moving much faster than Joey or I could work..

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2024-07-31

Kevin Rue-Albrecht (03:38:51) (in thread): > That would be awesome! It would be good to have guidance for both ‘regular’ shiny and ‘modular’ shiny in the Bioconductor guidehttps://contributions.bioconductor.org/shiny.htmlI suppose the page will just need a bit of reorganisation to interlace the two sets of shiny guidance. > I initially thought a section about ‘modules’ would be nice, but each of the existing sections would also deserve a note about testing, documentation, etc. for shiny modules - Attachment (contributions.bioconductor.org): Chapter 17 Shiny apps | Bioconductor Packages: Development, Maintenance, and Peer Review > Shiny apps can be submitted to Bioconductor as software packages or as documented and tested functions within packages. 17.1 Code organisation Shiny apps are divided into two parts: User…

2024-08-12

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2024-08-14

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2024-08-19

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2024-08-21

Louis Le Nézet (12:48:50): > Hi ! > I’m currently trying to test shiny modules with the shinytest2 package as mentionned in the guidelines of Bioconductor. > I’m facing a strange issue where my modules is working correctly when used directly but when used inrecord_test()it seems to be an old version of the module that seems to be used. > To test each modules separately I have amy_module_demo()function that return ashinyApp()when called and I pass this function to shinytest2 withrecord_test(my_module_demo()). > For some modules evertything works fine, but for some I need to change the name of the server function tomy_module_server2instead ofmy_module_serverfor the change to be applied. > As anyone faced a similar issue ? and how can I solve it ? > Thanks for your help !

Louis Le Nézet (13:31:09) (in thread): > I think the issue might come from the old version of my package that was installed in my library. > I’ve removed it, but now shinytest2 doesn’t work anymore tellingError in FUN(X[[i]], ...) : there is no package called 'Pedixplorer'even so that I usedload_all()andPedixplore::is available in the console.

Louis Le Nézet (13:53:58) (in thread): > So the issue was effectively due to shinytest2 using a new R session during testing. Therefore the package needs to be installed or to be load inside the demo function: > > if (isTRUE(getOption("shiny.testmode"))) { > pkgload::load_all(rprojroot::is_r_package$find_file()) > } > > This issue seems to be still in discussion#1 #2What would be the best approach ? - Attachment: #215 Trouble with namespace in application as package - Attachment: #264 Warnings from {golem} apps

2024-08-22

Maria Doyle (12:01:10): > fyihttps://genomic.social/@bioconductor/113006174034063087 - Attachment (genomic.social): Bioconductor (@bioconductor@genomic.social) > :rocket: We’re excited to share a blog post about deploying Shiny apps in Galaxy, thanks to a recent Bioconductor/Galaxy hackathon! Enhance your workflows with this collaboration. Read more: https://buff.ly/3WZ06dA > > Thanks to @galaxyproject@mstdn.science, @csoneson@fosstodon.org, @federicomarini, @bgruening@fosstodon.org, @hrhotz, and everyone involved! #UseGalaxy #Bioinformatics #Shiny #GalaxyProject > > Check out @galaxyfreiburg@xn–baw-joa.social’s post: https://buff.ly/3yQofLG

2024-09-10

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2024-10-23

Sounkou Mahamane Toure (11:49:39): > @Sounkou Mahamane Toure has joined the channel

2024-11-21

stefano mangiola (00:20:13): > @stefano mangiola has joined the channel

stefano mangiola (00:27:12): > Hello, I hope this is the right channel to post a shiny collaboration seeking. > > We are revamping our paper “A multi-organ map of the human immune system across age, sex and ethnicity” (details in the link) for an appeal to Cell Press rejection despite addressable feedback. Part of this feedback asks to create an interface (shiny) to communicate our results to the public. > > I am wondering if anyone is interested in collaborating. As the deadline is tight, we need an experienced shiny developer to pull this off (please in case share your shiny projects). The collaboration will be, of course, recognised with co-authorship. > > For more details, follow the linkhttps://github.com/stemangiola/shiny_immune_map_resultsPlease share to anyone possibly interested:pray:

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2024-11-22

Maria Doyle (04:22:48) (in thread): > If you don’t find a collaborator here and since your Shiny app involves Bioconductor packages, why not also post on the Bioconductor developers’ mailing list or in#developers-forum? It could give your project some good visibility among people who may not be in this channel but might be interested to collaborate.

Federico Marini (13:49:06): > @stefano mangiolahave you thought of deploying it with some form that leverage our iSEE “and friends”?

Federico Marini (13:50:02): > I am wondering whether you can have things cleverly put into the SE-like object and hop on a well oiled wheel

Federico Marini (13:50:36): > of course, if this “fits into an SE-like object”

stefano mangiola (18:34:46): > That’s an idea! The majority of the info would come as coefficient from a model, not so much from RNA counts. But it could be a further addition!

2024-11-23

Federico Marini (01:31:50): > still, as long as it’s rectangular…

Janani Ravi (09:32:16) (in thread): > Hi Stefano,we’veexperience with shiny apps and work in the micro immuno world.Please reach out.Let’stalk next week Janani.Ravi@cuanschutz.edu

2025-04-23

Louis Le Nézet (10:03:52): > Hi, I’ve developped a Shiny application in Pedixplorer and I’ve added helpfiles usingshinyhelperpackage. > These are markdown files stored in a folder and I’m wondering where should this folder be located in the package structure. > Should I put it at the root or in theinst/folder ?

Vince Carey (12:24:50): > great question@Marcel Ramos Pérezcould you have a look and propose a solution? sounds like we could need a guideline entry?

Marcel Ramos Pérez (12:48:03) (in thread): > The should be installed with the package to render on the fly. I’d say move them to theinst/folder and hopefullyshinyhelpercan find the files - File (PNG): image.png

2025-04-24

Louis Le Nézet (03:18:04) (in thread): > Thanks I moved them to “/inst/helpfiles” and used > > shinyhelper::observe_helpers( > help_dir = system.file("helpfiles", package = "Pedixplorer") > ) > > to force the location of the helpfiles.