AP-PLN is an automatic pipeline to design phenotypic linkage gene networks (AP-PLN) through the weighted combination of multiple functional datasets. This pipeline, is divided into three modules: the first creates a disease-specific phenotypic benchmark from a user-defined set of disease-relevant phenotype annotations, the second automates the evaluation and rescoring of each functional dataset on the phenotypic benchmark and the third combines different re-scored functional datasets into a final disease-specific phenotypic linkage network (PLN). AP-PLN also offers a visual comparison of individual functional datasets in terms of accuracy, the gene-pair coverage and a network representation for a subset of genes.
Running Automatic pipeline to build phenotypic linkage network (AP-PLN) requires at least Python (Python version 2.7.6) and R (R version 3.1.2). The following Python package must be installed: numpy (numpy version 1.9.1). The following R packages must be installed: earth (> 4.3.3), igraph (1.1.2) and biomaRt (2.30.0). As no compilation is required, the pipeline can be used on any computer, where Python and R are installed and it is therefore available for Windows, Linux, and MAC OS machines.
Using the buttons at the top of this page, download the ZIP file or the TAR ball, unzip/extract the download, and save the whole AP-PLN directory (folder) in your favorite directory.
The AP-PLN directory contains:
- A directory src with the source code of three modules and directories of python and R scripts.
- A user manual in pdf format.
The user must refer to the manual, which includes the installation instructions and a tutorial.
An automatic pipeline to design disease specific phenotypic linkage gene networks: AP-PLN
Viola Volpato; Caleb Webber; Cynthia Sandor