RAP is a rank aggregation-based data fusion approach for gene prioritization in plants. It can be used to perform the gene prioritization in Arabidopsis thaliana and 28 non-plant species. The input of RAP are a set of genes of interest and the network-based gene prioritization results from AraNet v2 system, while the output are the ranks of cand…
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DESCRIPTION
LICENSE
NAMESPACE
RAP-Reference-Manual.pdf
RAP_User_Manual.pdf
README.md
SampleData_AraNetPred.txt

README.md

RAP

RAP is a rank aggregation-based data fusion approach for gene prioritization in plants. It can be used to perform the gene prioritization in Arabidopsis thaliana and 28 non-plant species. The input of RAP are a set of genes of interest and the network-based gene prioritization results from AraNet v2 system, while the output are the ranks of candidate genes. RAP has been successfully applied to prioritize flowering-time genes in Arabidopsis. The genome-wide experimental results indicate that RAP can be used as a complement to the network-based gene prioritization algorithm (e.g., AraNet v2) for accurately prioritizing candidate genes underlying biological processes or agricultural traits.

Installation

  • Note: R package "devtools" is required to install RAP package from github.
require("devtools")
install_github("cma2015/RAP")

How to use

Please refer to https://github.com/cma2015/RAP/blob/master/RAP-Reference-Manual.pdf for details about each function.

Contact

If any suggestions are available, feel free to contact: Zhai Jingjing(zhaijingjing603@gmail.com)

Citation

Zhai, J., Tang, Y., Yuan, H., Wang, L., Shang, H., & Ma, C. (2016). A meta-analysis based method for prioritizing candidate genes involved in a pre-specific function. Frontiers in plant science, 7, 1914.