PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw re

chayan · 10-14-2015, 02:40 AM

Which utility package (preferable web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw reads ??? I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable...

gringer · 10-14-2015, 10:52 AM

FactoMineR does a lot of great PCA things, and can fairly easily produce nice plots:

http://factominer.free.fr/classical-...-analysis.html

According to the FactoMineR main page, there's also now Factoshiny, which provides a dynamic, interactive way to explore your data with FactoMineR:

http://factominer.free.fr/

Quote:

I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable

You're posting in a bioinformatics forum, and rubbishing the free software swiss army statistics chainsaw of R. Saying "R is too confusing, can you tell me how I can do [statistics] without using R" is unlikely to give you good results.

chayan · 10-14-2015, 12:13 PM

No not at all rubbishing..sorry if I misunderstood...i just said as i am not a bioinformatician so i found it tough to use..anyway thanks for your suggestion

cliffbeall · 03-02-2017, 06:28 AM

Since this is one of the top hits while googling, thought I would leave here that CheckM with the tetra_pca command will do this:

https://github.com/Ecogenomics/CheckM/wiki/Plots

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10-14-2015, 02:40 AM	#1
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw re Which utility package (preferable web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw reads ??? I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable...

10-14-2015, 12:13 PM	#3
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	No not at all rubbishing..sorry if I misunderstood...i just said as i am not a bioinformatician so i found it tough to use..anyway thanks for your suggestion

03-02-2017, 06:28 AM	#4
cliffbeall Senior Member Location: Ohio Join Date: Jan 2010 Posts: 144	Since this is one of the top hits while googling, thought I would leave here that CheckM with the tetra_pca command will do this: https://github.com/Ecogenomics/CheckM/wiki/Plots