PIPE

An R package PIPE

@ Overview

The PIPE is a pleiotropy-driven framework for therapeutic target prediction and validation, with its validity illustrated using two systems of disorders as exemplars, generating pleiotropy target resources for neuropsychiatric disorders and inflammatory disorders, respectively. Also made available are functional modules and prioritisation map.

@ Installation

1. Install R

Please install R (version 4.3.2 or above); see https://cran.r-project.org

If installed on Ubuntu (assuming you have a ROOT (sudo) privilege), please do so below

sudo su
# here enter your password

wget http://www.stats.bris.ac.uk/R/src/base/R-4/R-4.3.2.tar.gz
tar xvfz R-4.3.2.tar.gz
cd ~/R-4.3.2
./configure
make
make check
make install
R # start R

2. Install R packages

R # start R

# if the package 'BiocManager' not installed, please do so
if(!("BiocManager" %in% rownames(installed.packages()))) install.packages("BiocManager")

# first, install basic packages: remotes, tidyverse
BiocManager::install(c('remotes','tidyverse'), dependencies=T)

# then, install the package 'PIPE' (now hosted at github)
BiocManager::install("hfang-bristol/PIPE", dependencies=T, force=T)

# check the package 'PIPE' successfully installed
library(PIPE)

@ Showcases

Showcases, describing step-by-step instructions, are made reproducible for neuropsychiatric disorders, inflammatory disorders, functional modules, and prioritisation map.

@ Contact

Please drop email for bug reports or enquiries.

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