New data and workflow.

A new version of DairyFMBN has been added to Mendeley data (https://data.mendeley.com/datasets/3cwf729p34/5) and quarantine will expire at the end of July. This is connected to an astounding ( 😉 )workflow for inference of microbial association networks, which is available on GitHub (https://github.com/ep142/MAN_in_cheese). Both are related to a review on microbial association networks in cheese which is about to be published as a preprint…

ShinyFMBN 2.1.2 is available for download

The development version of ShinyFMBN 2.1.2 (I had time only for limited testing) is available for download. The app includes access to records of FoodMicrobionet 3.1 and a new version of the manual is available. If you have time to test it please do and let me know:

  • if you find a bug provide enough information to reproduce the error
  • if your testing is successful (i.e. everything seems to work smoothly) please let me know which machine, operating system, browser and R version you have used for testing (see examples on page 11 of the manual)

New graphs in the app!

Now ShinyFMBN (v2.1.2) can produce directly a number of useful exploratory graphs, including prevalence and abundance plots, bar plots of taxa abundance and box/violin plots for taxa abundance. All the graphs can be personalised.

a stacked bar plot for OTU abundance
a box plot of the most abundant and prevalent taxa
A violin plot of the most abundant and prevalent taxa: the level of aggregation can be personalised and the taxa to be displayed can be selected from a menu.

The new app will be released in February 2020.

FMBN2MBanalyst

This is a new script for converting *_agg.RDS or *_physeq.Rdata files created using the ShinyFMBN app (v1.1 or later) in OTU, taxonomy and sample metadata tables suitable for use with the Marker Data Profiling analysis pipeline of Microbiome Analyst (https://www.microbiomeanalyst.ca). Click here to download. Please beware: I am too old to be willing to write foolproof scripts and try to predict the vagaries of lazy users. If you are a fool (and/or don’t read/follow the instructions provided as comments in the script) the script will not work. Period.

ShinyFMBN, a Shiny app for exploring FoodMicrobionet v 3.0

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:

  1. explore studies in FoodMicrobionet;
  2. filter samples to extract a subset of the database;
  3. (optionally) aggregate taxa or samples;
  4. export data (OTU abundance tables) and metadata in a variety of formats:
    1. .RDS files for further analysis
    2. a phyloseq class object for use with Shiny-phyloseq
    3. a .gml file for use in Gephi and Cytoscape
    4. 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.

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