ShinyFMBN, a Shiny app to access FoodMicrobionet
This data set contains the ShinyFMBN app and related material. The ShinyFMBN app allows you to access FoodMicrobionet 3.1, a repository of data on food microbiome studies. To run the app you need to install R and R Studio. This compressed folder contains: a. folder data: contains a .RDS file of data extracted from FoodMicrobionet, to be used with the FMBNanalyzer script (see below) b. folder FMBNanalyzer: contains the FMBNanalyzer_v_2_1.R which can be used for graphical and statistical analysis of data extracted from FoodMicrobionet c. folder Gephi_network: contains a .gml file extracted from FoodMicrobionet using the ShinyFMBN app, a .gephi file created by importing it, and an example figure of the network d. folder merge_phyloseq_objs: contains a proof of concept script which can be used to merge phyloseq objects extracted from FoodMicrobionet using the ShinFMBN app, together with example data e. folder ShinyFMBN contains the app folder, the runShinyFMBN_2_1_4.R script (a R script to install all needed packages and run the app) and the app manual in .htm format This version includes an improved version of the Shiny app and incorporates changes to the taxa table, which is now aligned to SILVA taxonomy (https://www.arb-silva.de/documentation/silva-taxonomy/). This change has become necessary to improve compatibility with new accessions to FoodMicrobionet, which now assigns taxonomy based on SILVA v138.
Steps to reproduce
Read carefully the instructions provided in the manuals and the scripts.