SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Co-occurrence analysis Francy87 Bioinformatics 0 10-01-2013 01:14 AM
Guide/tutorial for the analysis of RNA-seq data MDY Bioinformatics 70 07-22-2013 11:57 PM
RNA-Seq: The bench scientist's guide to statistical analysis of RNA-Seq data. Newsbot! Literature Watch 0 09-18-2012 02:00 AM
Idiots guide to setting up Amazon instance for sequence analysis 454newbie Bioinformatics 7 06-08-2011 12:31 PM
PubMed: Pyrosequencing analysis of endosymbiont population structure: co-occurrence o Newsbot! Literature Watch 0 04-29-2009 05:00 AM

Reply
 
Thread Tools
Old 03-24-2014, 10:48 AM   #1
Gorbenzer
Member
 
Location: italy

Join Date: Apr 2012
Posts: 45
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!
Gorbenzer is offline   Reply With Quote
Old 03-26-2014, 05:52 AM   #2
cliffbeall
Senior Member
 
Location: Ohio

Join Date: Jan 2010
Posts: 144
Default

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
cliffbeall is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:50 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO