Question: PCA Tools to analyse RNA-seq data
0
gravatar for vasanth.m.29
9 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 • 708 views
ADD COMMENTlink modified 4 months ago by Jennifer Pham140 • written 9 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 9 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 4 months ago by b.nota4.9k
1
gravatar for TriS
9 months ago by
TriS3.4k
United States, Buffalo
TriS3.4k wrote:

MeV is a good start

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

ADD COMMENTlink written 9 months ago by TriS3.4k

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

ADD REPLYlink written 9 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 9 months ago by TriS3.4k
1
gravatar for Jennifer Pham
4 months ago by
Jennifer Pham140
San Diego CA
Jennifer Pham140 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 4 months ago by Jennifer Pham140
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