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Old 10-14-2015, 01:40 AM   #1
chayan
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Unhappy 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...
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Old 10-14-2015, 09:52 AM   #2
gringer
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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.
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Old 10-14-2015, 11:13 AM   #3
chayan
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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
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Old 03-02-2017, 05:28 AM   #4
cliffbeall
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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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kmerfreq, ngs data analysis, pca plot, r package, tetranucleotide

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