Can anyone suggest a RShiny app for displaying RNA-seq results online

Question

[BioinfGuru]

Im currently building an RShiny app to display our RNA-seq analysis data online. No point in reinventing the wheel, so if anyone knows of the location of an app already built and open source then let me know

Regards, Kenneth

Answer 1

[WouterDeCoster]

If you haven't decided on your workflow, kallisto + sleuth has a shiny output.

[BioinfGuru]

my group has actually tried this...however there is a very common error they got stuck at that appears to have no resolution yet ... something to do with X11 im not sure.

[WouterDeCoster]

Well it worked for me...

Answer 2

[Istvan Albert]

See also the "Lair" at Lior Pachter's lab

This website houses a database providing interactive access to the (re)analysis of publicly available RNA-Seq data presented in published papers. The resource is powered by kallisto, sleuth, the Snakemake workflow management system and the Shiny web application framework. GitHub repositories with the source code for the project are located at bears_analyses and lair.

http://pachterlab.github.io/lair/analyses/

[BioinfGuru]

Unfortunately sleuth requires quantification with Kalisto...while ours is a tophat/cufflinks/cuffdiff pipeline.

[Lior Pachter]

I strongly recommend you replace your tophat+cufflinks+cuffdiff2 pipeline with kallisto+sleuth.

[BioinfGuru]

Agreed, but my hands are tied on this one...it is part of a university project to replicate someone else's data with the pipeline they use.

thanks though

[Fill]

Why kallisto+sleuth is better than tophat+cufflinks+cuffdiff2 pipeline?

Answer 3

[Charles Plessy]

How about iDEP ? It has nice documentation and manucript. It offers heatmap, k-means, PCA, differential expression analysis, pathway analysis, biclustering, and more.

Answer 4

[h.mon]

This is an old post, and my answer is not what the OP wants (I think it is Ruby on Rails, not Rshiny), but Degust seems really nice.