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  • co-occurrence analysis guide / software

    Dear all,
    i'm looking for a guide / software for co-occurrence and co-exclusion analysis of 16S profiling tabular data and RnaSeq/Microarray expression tabular data.

    Anyone have any suggestion?

    Thank you so much!

  • #2
    This is an interesting question. We are pretty interested in this topic and there seem to be a large number of approaches.

    There is this reference:
    Microbial Co-occurrence Relationships in the Human Microbiome

    Someone from that lab gave me some of the code they had used. There are also some functions in the R package vegan to calculate checkerboard scores and generate Null model communities. Try ?nestedchecker and ?oecosimu.

    Edit: By the way, what are you going to do with RNAseq/microarray data?
    Last edited by cliffbeall; 03-26-2014, 05:54 AM. Reason: Add a thought

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