add readme

README.Rmd

@@ -19,37 +19,34 @@ knitr::opts_chunk$set(
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 <!-- badges: end -->
 
-The goal of affiliationExplorer is to ...
+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:
 
-```{r cars}
-summary(cars)
+``` r
+## install.packages("remotes")
+remotes::install_github("mahendra-mariadassou/affiliationExplorer")
 ```
 
-You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date.
+## Launching the app
 
-You can also embed plots, for example:
+You can launch on your computer as follows:
 
-```{r pressure, echo = FALSE}
-plot(pressure)
+```{r example, eval = FALSE}
+library(affiliationExplorer)
+affiliationExplorer::run_app()
 ```
 
-In that case, don't forget to commit and push the resulting figure files, so they display on GitHub!

README.md

+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# affiliationExplorer
+
+<!-- badges: start -->
+
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+<!-- badges: end -->
+
+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](https://github.com/mahendra-mariadassou/phyloseq-extended/tree/dev)
+
+**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](https://github.com/mahendra-mariadassou/affiliationExplorer)
+with:
+
+``` r
+## install.packages("remotes")
+remotes::install_github("mahendra-mariadassou/affiliationExplorer")
+```
+
+## Launching the app
+
+You can launch on your computer as follows:
+
+``` r
+library(affiliationExplorer)
+affiliationExplorer::run_app()
+```