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. You can visit an example
instance of the application here where the
method is used to find new
TPE-OLD candidate
genes based on the currently known ones.
This package depends on geposan,
which should be installed first.
You can install the development version of geposanui using:
# install.packages("remotes")
# remotes::install_github("johrpan/geposan")
remotes::install_github("johrpan/geposanui")See this page for more information on this command.
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:
# 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).
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
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 for more details.