Easy differential expression heatmap?
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Entering edit mode
6 weeks ago
Amy • 0

I'm finally getting back to an RNAseq differential expression dataset I analyzed years ago and cannot remember what tool I used to generate these simple heat maps that I really like. I think it was an online interface where I could add/take away genes from the plot, alter comparison groups, pick options for significance symbols etc. It may have had the ability to filter by GO terms, or I may have used a different source (e.g., GSEA) to pick my genes and then just used this tool for the plots. I'm very rusty on this stuff and would be very grateful if someone can direct me back to this or a similar user-friendly tool. Thank you!

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Entering edit mode
6 weeks ago
ivivek_ngs ★ 5.1k

I would recommend to get something programmatically so that you can play around the different distance metrics while making any heatmaps since with such click based tools often that is not possible if they are not parameterized for such. For click based on gene expression profile try heatmapper.

If you want more comprehensive tool, I would recommend AltAnalyzer. Seems like it does beyond heatmap and has a suite of tools and algorthims. There are nice detailed tutorials (RNASeq) availabe that are both video and vignette based.

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Entering edit mode
5 weeks ago
M.O.L.S ▴ 40

You could possibly use the pheatmap library in R, if you stilll have the data.

enter code here:

library(pheatmap)
library(viridis)

pheatmap( insert your dataset here , color=viridis::viridis(100))