README.md

In twesleyb/getPPIs: Compile from the HitPredict Database

getPPIs

Description

getPPIs is an R package containing a compilation of experimentally identified, confidence scored protein-protein interactions (PPIs) from HitPredict. Simply load a data.frame containing the PPI data using data(musInteractome) or data(hsInteractome).

For more information about HitPredict, please see authors' original publications: Lopez et al., 2015 [1] Patil et al., 2011 [2] * Patil and Nakamura 2005 [3]

Installation

In R, download getPPIs from GitHub:

devtools::install_github("twesleyb/getPPIs")

Usage

library(getPPIs)

# load the HitPredict dataset
data(hsInteractome)

# load the HitPredict dataset, mapped to mouse genes
data(musInteractome)

References

[1] Patil, A. & Nakamura, H. Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 6, 100 (2005).

[2] Patil, A., Nakai, K. & Nakamura, H. HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39, D744-9 (2011).

[3] López, Y., Nakai, K. & Patil, A. HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. Database (Oxford) 2015, (2015).

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

twesleyb/getPPIs documentation built on Jan. 2, 2021, 5:59 p.m.