RNA-seq visualization tools

Question

[maeva.giraudo]

Hi all, What would be your best/preferred/go-to method or tool for presenting RNA-seq results for differentially expressed genes?

I have been working with RNA-seq for a few years now to identify genes responding to contaminants in fish but I am feeling stuck in the same pattern of data visualization and presentation for publication involving volcano plots, GO enrichment and boxplots. I am looking for some new inspiration!.

Any suggestion will be greatly appreciated :)

Maeva

Answer 1

[zizigolu]

http://wiki.c2b2.columbia.edu/workbench/index.php/Home

A simple and good workbench that I have already used to draw volcano plot, but has much more options

simply download, install, upload list of differentially expressed genes, determine control and treatment samples, finally by t-test you would be able to draw many relevant plots. about GO, I use Cytoscape-BINGO plugin. simply copy and paste the list of your differentially expressed genes and a plot of GO would be illustrated. I have also used PANTHER for drawing chart of GO terms, very simple

http://pantherdb.org/