mirror of
https://github.com/johrpan/geposanui.git
synced 2025-10-26 03:07:24 +01:00
79 lines
2.8 KiB
Markdown
79 lines
2.8 KiB
Markdown
# geposanui
|
|
|
|
This R 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://github.com/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
|
|
|
|
This package depends on [`geposan`](https://github.com/johrpan/geposan'),
|
|
which should be installed first.
|
|
|
|
You can install the development version of `geposanui` using:
|
|
|
|
```r
|
|
# install.packages("remotes")
|
|
# remotes::install_github("johrpan/geposan")
|
|
remotes::install_github("johrpan/geposanui")
|
|
```
|
|
|
|
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`).
|
|
|
|
## Publication
|
|
|
|
This method and its implementation have been peer-reviewed and published in
|
|
NAR Genomics and Bioinformatics. If you use the package in your research or
|
|
would like to refer to our methodology, please cite the following paper:
|
|
|
|
Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller, Proposing
|
|
candidate genes under telomeric control based on cross-species position data,
|
|
NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae037,
|
|
https://doi.org/10.1093/nargab/lqae037
|
|
|
|
## 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.
|