A manuscript related to FoodMicrobionet has just been published.
De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018. A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota. International Journal of Food Microbiology. 265:9-17 https://doi.org/10.1016/j.ijfoodmicro.2017.10.028
Look here. Free downloads (until Dec. 24th, 2017) here.
ShinyFMBN, a Shiny app for exploring, filtering and extracting data from FoodMicrobionet v 3.0 is here…
With this app you will be able to:
- explore studies in FoodMicrobionet;
- filter samples to extract a subset of the database;
- (optionally) aggregate taxa or samples;
- export data (OTU abundance tables) and metadata in a variety of formats:
- .RDS files for further analysis
- a phyloseq class object for use with Shiny-phyloseq
- a .gml file for use in Gephi and Cytoscape
- OTU and sample tables ready for import in the CoNet app of Cytoscape
You can download the first version of the manual here. You can download the beta here. Unfortunately I did not have the time for extensive testing so, if you notice something strange let me know. In the message please provide your name, affiliation, current position, and drop a few lines on why you are interested in the app.
I am working on a major revision of the database and scripts (eventually access and analysis will be through Shiny apps). If there is any major feature you would like to see in the new version let me know.