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Old 03-24-2014, 10:48 AM   #1
Location: italy

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Default 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!
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Old 03-26-2014, 05:52 AM   #2
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Location: Ohio

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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 at 05:54 AM. Reason: Add a thought
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