Visualization of RNA-SEQ Analysis

Question

[ashwing.kofficial]

Hello guys,

I just finished my undergrad project which consists of pathway study of a disease using Rna-seq data. To publish the paper, I though I could use a few images for the analysis. Is there any good visualization software for Rna-seq data where I can use my degs for visualization.

[Carlo Yague]

I know of at least two tools to visualize enriched pathways: DAVID , which is a bit old but still useful last time I checked, and reactome.org which provide really nice illustration of protein pathways.

[ashwing.kofficial]

I have used DAVID before but it is not capable of visualization tools, but gives a detailed analytical report. I am looking for visuals which represent an overall aspect. Also,Reactome is more specific than DAVID

[Carlo Yague]

You can visualize pathway enrichment with DAVID. It shows DE genes (highlighted with a red star) on full KEGG pathways, for instance like this:

Is it what you are looking for or were you thinking of a different kind of "images for pathways analysis".

[ashwing.kofficial]

No sir, I already have that, I am looking for an image which can illustrate the DEGS in a summarized manner.

[Carlo Yague]

Sorry I misunderstood, but then it is still unclear for me what you are looking for.

Answer 1

[Michał]

Hey, try PathfindR package from R. https://cran.r-project.org/web/packages/pathfindR/vignettes/intro_vignette.html

[ashwing.kofficial]

I will have a look at it, thank you