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79 lines
2.8 KiB
Markdown
79 lines
2.8 KiB
Markdown
# geposanui
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This R package provides a graphical user interface for analyzing genes based
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on position data across species. It is a frontend for the R package
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[`geposan`](https://github.com/johrpan/geposan). You can visit an example
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instance of the application [here](https://tpe-old.uni-rostock.de) where the
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method is used to find new
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[TPE-OLD](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233240/) candidate
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genes based on the currently known ones.
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## Installation
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This package depends on [`geposan`](https://github.com/johrpan/geposan'),
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which should be installed first.
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You can install the development version of `geposanui` using:
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```r
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# install.packages("remotes")
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# remotes::install_github("johrpan/geposan")
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remotes::install_github("johrpan/geposanui")
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```
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See [this page](https://remotes.r-lib.org/reference/install_git.html) for more
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information on this command.
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## Usage
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The main entry point is the `run_app()` function that is provided by the
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package. It will setup the initial analysis and provide the interactive user
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interface. You have to provide at least one gene set for the application to
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work. The following minimal example shows how to do that:
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```r
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# Ten random genes from Ensembl.
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my_interesting_genes <- c(
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"ENSG00000142347",
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"ENSG00000186174",
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"ENSG00000143553",
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"ENSG00000240972",
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"ENSG00000105357",
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"ENSG00000159251",
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"ENSG00000258643",
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"ENSG00000147873",
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"ENSG00000158270",
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"ENSG00000197616"
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)
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# Choose a name for your gene set.
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geposanui::run_app(list("Interesting genes" = my_interesting_genes))
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```
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This will run the application which you can reach using your favorite browser.
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For more information on the options provided by the function, take a look at the
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built-in documentation (`?geposanui::run_app`).
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## Publication
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This method and its implementation have been peer-reviewed and published in
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NAR Genomics and Bioinformatics. If you use the package in your research or
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would like to refer to our methodology, please cite the following paper:
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Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller, Proposing
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candidate genes under telomeric control based on cross-species position data,
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NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae037,
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https://doi.org/10.1093/nargab/lqae037
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## License
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This program is free software: you can redistribute it and/or modify it under
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the terms of the GNU Affero General Public License as published by the Free
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Software Foundation, either version 3 of the License, or (at your option) any
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later version.
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This program is distributed in the hope that it will be useful, but WITHOUT ANY
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WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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PARTICULAR PURPOSE. See the
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[GNU Affero General Public License](https://www.gnu.org/licenses/agpl-3.0.html)
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for more details.
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