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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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FactoMineR does a lot of great PCA things, and can fairly easily produce nice plots:
According to the FactoMineR main page, there's also now Factoshiny, which provides a dynamic, interactive way to explore your data with FactoMineR:
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.I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable -
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 suggestionComment
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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:
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