Heatmap and rna-seq

Question

[qudrat.nii]

Hello everyone!

I have a list of pathways from GSEA analysis (RNA-Seq data) and I want to plot a heatmap of genes associated with pathways, showing distinctly each pathway in the heatmap. Can somebody help me with this

Answer 1

[pinheirofabiano]

install.packages("pheatmap")

library(pheatmap)

setwd("/Users/data_analysis/results")

data <- read.table(file = "log2cpm.tsv", header = T, sep = "\t")

pheatmap(mat = data)

Answer 2

[dsull]

Check out clustergrammer from Avi Ma'ayan's lab.

[GenoMax]

Please include a link when you are recommending a tool. There can be programs with similar names.

[dsull]

https://maayanlab.cloud/clustergrammer/

It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pathway x gene matrix or a sample x gene matrix.

Answer 3

[Kevin Blighe]

Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap.

You have not indicated that you require assistance with coding; so, I will end my answer right here.

Kevin