geposan

Geposan is an R package for analyzing genes based on their position across species. The package includes gene data from Ensembl. It provides multiple methods to use that data to find genes that score well in comparison with a set of reference genes.

Installation

You can install the development version of geposan using:

# install.packages("remotes")
remotes::install_github("johrpan/geposan")

See this page for more information on this command.

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

Graphical interface

Please also take a look at the interactive graphical web interface for geposan which is available as a separate R package called geposanui.

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 for more details.