affiliationExplorer

The goal of affiliationExplorer is to provide a user-friendly graphical interface to choose between different conflicting affiliations.

You need to provide to upload two files to the application:

a biom file
a multihits file (typically called multihits_blabla.tsv)

The app will then sort the multi-affiliated taxa from most abundant to least abundant and help you pick one (or none) of the conflicting affiliations. You can also edit the affiliation manually.

Finally, use the Download button to download the biom file with corrected affiliations. This cleaned biom can be parsed with import_frogs() from the phyloseq.extended package

Note affiliationExplorer uses short taxa names, which may differ from the original names, in the display. However, names from the original biom file are preserved in the cleaned biom.

Installation

You can install the latest version of affiliationExplorer from github with:

## install.packages("remotes")
remotes::install_github("mahendra-mariadassou/affiliationExplorer")

Launching the app

You can launch on your computer as follows:

library(affiliationExplorer)
affiliationExplorer::run_app()