Differential gene analysis from a javascript based web app
I have two subsets of cells and their gene expression in a web app written in javascript. I need a way now to determine which genes are differentially expressed between the groups. I searched for javascript libraries but found nothing, so I reasoned to try using OpenCPU to call an R script located on my server. How could I call R script on the server from my javascript- based app, receive several parameters in the script, and then send back the results to the front end?
Also asked here: https://bioinformatics.stackexchange.com/questions/5059/find-differentially-expressed-genes-from-a-web-app
• 2,237 views
•
link
written
by
nikitavlassenko
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to properly use DESeq2 for an experiment
written by Aurélien •
-
Create a regulatory network between exosomal and endogenous miRNAs
written by diego1530 •
-
Interpretation of normalized counts
written by ika •
-
How do I identify which differentially expressed genes are on the cell surface?
written by charlesgwellem •
-
Gene correlation analysis after deseq2
written by Biogeek
-
FPKM and DESEq - RNAseq
written by carolgalah •
-
DESeq2 question: how to identify genes expressed only in one condition
written by EVWS •
-
A Heatmap based on RPKM values of log2fold change?
written by Mehmet
-
How to calculate chromosomal enrichment of differentially expressed genes
written by Sakti
-
Rpkm Or Fpkm For Paired End Data Analyses Of Gene Expression?
written by Nebo •
Javascript is not meant to do heavy duty analyses like this. R only runs on a server, maybe you can expose a web service to accept data for analysis and return analyzed results, but don't try to run R from a browser.
JavaScript is for client side processing, you don't want to rely on your client's processing power/browser stability/JS settings for data analysis.
What about server-side javascript? I have
node.json the server. Maybe there are any other libraries in other languages that could be accessed easily from javascript? LikeC++, idk... I actually think thatOpenCPUis the right way to go, I am just not sure how to call it on the server from my javascript appSearching for "gene expression javascript webapp" leads me to many seemingly good hits, among them DEIVA: a web application for interactive visual analysis of differential gene expression profiles and UBiT2: a client-side web-application for gene expression data analysis. I am sure you can gather some ideas from these projects. Or maybe you want to use shiny for this, as in shinyGEO: a web-based application for analyzing gene expression omnibus datasets.
I need something like this: https://docs.microsoft.com/en-us/machine-learning-server/deployr/deployr-about But I do not want to use DeployR server itself, just need such an API.
Only R shiny has a persistent always-listening server, which is what you need for R scripts on demand. You can write a PHP page that runs an R script and returns the result, and call this PHP page from JavaScript, if you'd like. Just be aware that parameters and results need to be passed as plain text (say JSON) and it will open your server wide to bot attacks that can throw random data at the PHP page running the R process.