How to compare RNA expression correlation?
1
0
Entering edit mode
21 months ago
Wang Cong ▴ 10

I have a set of genes that is important for the cell cycle and DNA damage. I wish to compare the RNA expression of these genes between each two cell lines and generate a heatmap to visualize the correlation (the x and y axis are all types of cancer cell lines). May I ask if there are any software/packages to do this task? Thanks!

enter image description here

RNA-seq cancer-cell-line correlation • 439 views
ADD COMMENT
0
Entering edit mode
21 months ago
Trivas ★ 1.8k

You'll want to use a differential gene expression software (DESeq2, edgeR, etc.) then take the output or normalized counts for downstream analyses. I like using the package ComplexHeatmap since it's easier to customize than pheatmap

ADD COMMENT

Login before adding your answer.

Traffic: 1654 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6