PCA Tools to analyse RNA-seq data

Question

[vasanth.m.29]

Hi,

I have performed RNA-seq data analysis. pipeline TopHap > Cufflinks > Cuffcompare > Cuffdiff I would like to do PCA for the cuffdiff output data. Can anyone suggest any tool to do PCA that does not involve R packages and in Linux environment?

Thanks.

[biofalconch]

Have you checked the funtion prcomp?

You can read more about it here: https://www.r-bloggers.com/principal-component-analysis-in-r/

Also, if you ever change your mind on not using R pakages, might want to check mixOmics

[Benn]

Why exclude R? R is one of the most popular languages in bioinformatics, excluding that language will make your analysis only more difficult...

Answer 1

[TriS]

MeV is a good start

http://mev.tm4.org/#/welcome

[vasanth.m.29]

Can you please provide the link to Linux version of MeV.

[TriS]

the linked version is a web-based application. the desktop application is a standalone java-based version

Answer 2

[Jennifer Pham]

Hi, i think BioVinci can work for you. It supports Ubuntu and the PCA function over there does not required any coding. You can find it here: https://vinci.bioturing.com/