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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...

  • #2
    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:

    FactoMineR, an R package dedicated to multivariate Exploratory Data Analysis


    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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    • #3
      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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      • #4
        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:

        Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes - Ecogenomics/CheckM

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