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PCA Tools to analyse RNA-seq data

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.

rna-seq pca
• 4,920 views • link
updated by Jennifer Pham Jennifer Pham • written by vasanth.m.29 • vasanth.m.29

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

• 1 views • link
written by Benn Benn

2 answers

MeV is a good start

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

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written by TriS TriS

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

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written by vasanth.m.29 • vasanth.m.29

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

• 0 views • link
written by TriS TriS

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/

enter image description here

• 1 views • link
written by Jennifer Pham Jennifer Pham

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