Question: PCA Tools to analyse RNA-seq data
0
gravatar for vasanth.m.29
12 months ago by
vasanth.m.290 wrote:

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 • 827 views
ADD COMMENTlink modified 7 months ago by Jennifer Pham260 • written 12 months ago by vasanth.m.290

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

ADD REPLYlink written 12 months ago by biofalconch390

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

ADD REPLYlink written 7 months ago by b.nota5.4k
1
gravatar for TriS
12 months ago by
TriS3.5k
United States, Buffalo
TriS3.5k wrote:

MeV is a good start

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

ADD COMMENTlink written 12 months ago by TriS3.5k

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

ADD REPLYlink written 12 months ago by vasanth.m.290

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

ADD REPLYlink written 12 months ago by TriS3.5k
1
gravatar for Jennifer Pham
7 months ago by
Jennifer Pham260
San Diego CA
Jennifer Pham260 wrote:

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

ADD COMMENTlink written 7 months ago by Jennifer Pham260
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