The goal of affiliationExplorer is to provide a user-friendly graphical interface to choose between different conflicting affiliations.
## Installation
You need to provide to upload two files to the application:
You can install the released version of affiliationExplorer from [CRAN](https://CRAN.R-project.org) with:
- a `biom` file
- a multihits file (typically called `multihits_blabla.tsv`)
``` r
install.packages("affiliationExplorer")
```
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.
## Example
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](https://github.com/mahendra-mariadassou/phyloseq-extended/tree/dev)
This is a basic example which shows you how to solve a common problem:
**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.
```{r example}
library(affiliationExplorer)
## basic example code
```
## Installation
What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
You can install the latest version of `affiliationExplorer` from [github](https://github.com/mahendra-mariadassou/affiliationExplorer) with: