# geposanui

This package provides a graphical user interface for analyzing genes based on
position data across species. It is a frontend for the R package
[`geposan`](https://code.johrpan.de/johrpan/geposan). You can visit an example
instance of the application [here](https://tpe-old.uni-rostock.de) where the
method is used to find new
[TPE-OLD](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233240/) candidate
genes based on the currently known ones.

## Installation

You can install the development version of `geposanui` using:

```r
# install.packages("remotes")
remotes::install_git("https://code.johrpan.de/johrpan/geposanui.git")
```

See [this page](https://remotes.r-lib.org/reference/install_git.html) for more
information on this command.

## Usage

The main entry point is the `run_app()` function that is provided by the
package. It will setup the initial analysis and provide the interactive user
interface. You have to provide at least one gene set for the application to
work. The following minimal example shows how to do that:

```r
# Ten random genes from Ensembl.
my_interesting_genes <- c(
    "ENSG00000142347",
    "ENSG00000186174",
    "ENSG00000143553",
    "ENSG00000240972",
    "ENSG00000105357",
    "ENSG00000159251",
    "ENSG00000258643",
    "ENSG00000147873",
    "ENSG00000158270",
    "ENSG00000197616"
)

# Choose a name for your gene set.
geposanui::run_app(list("Interesting genes" = my_interesting_genes))
```

This will run the application which you can reach using your favorite browser.
For more information on the options provided by the function, take a look at the
built-in documentation (`?geposanui::run_app`).

## License

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option) any
later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the
[GNU Affero General Public License](https://www.gnu.org/licenses/agpl-3.0.html)
for more details.
