What documentation/paperwork/approvals are necessary to share parts of the Microbiome RIG dataset for a subgroup analysis?

1. Email daniel.spakowicz@osumc.edu to discuss the concept and find time on the Microbiome RIG agenda

2. Present to the RIG ( to check overlap, assess feasibility, and provide feedback)

3. Processed microbe annotations for the Avatar patients can be shared without additional documentation

4. If an investigator needs to access the raw Avatar data files that you are using for a subproject that they want to propose, here are the steps:

   1. They fill out the RIG sub-project proposal form, which the Microbiome RIG and Aster will review to check overlap, assess feasibility, and provide feedback.

   2. Aster sends out the proposal to the RIG members and OPMs and gives a two-week grace period to allow any institution to express if they want to “opt out” for that specific project (which has never happened, but if it did, we would exclude their cases from the dataset)

   3. After the two-week grace period, Aster provides access to the dataset or provisions the required subset of data and provides access to the investigator.

How can I create a phyloseq object from the exORIEN output?

Phyloseq is a bioconductor package with functions for standard microbiome analyses. The relative abundances from the Bracken output can be converted into "OTU table" and "taxonomy table" objects and then used to generate a phyloseq object using the github gist found here. 

How can I request that an expression signature be calculated for the entire dataset? 

Expression signatures are being managed through the R package “tmesig”. To request an additional signature please post an issue on GitHub repo: https://github.com/spakowiczlab/tmesig/issues