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Pi

This is the development version of Pi; for the stable release version, see Pi.

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level


Bioconductor version: Development (3.19)

Priority index or Pi is developed as a genomic-led target prioritisation system. It integrates functional genomic predictors, knowledge of network connectivity and immune ontologies to prioritise potential drug targets at the gene and pathway level.

Author: Hai Fang, the ULTRA-DD Consortium, Julian C Knight

Maintainer: Hai Fang <hfang.shanghai at gmail.com>

Citation (from within R, enter citation("Pi")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Pi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Pi")
Pi User Manual (R/Bioconductor package) HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneTarget, Genetics, GenomeWideAssociation, GraphAndNetwork, HiC, LinkageDisequilibrium, Network, Pathways, Software
Version 2.15.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends igraph, dnet, ggplot2, graphics
Imports Matrix, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, lattice, caret, plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr, tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble
System Requirements
URL http://pi314.r-forge.r-project.org
Bug Reports https://github.com/hfang-bristol/Pi/issues
See More
Suggests foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite
Linking To
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Pi_2.15.0.tar.gz
Windows Binary Pi_2.15.0.zip
macOS Binary (x86_64) Pi_2.15.0.tgz
macOS Binary (arm64) Pi_2.15.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Pi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Pi
Bioc Package Browser https://code.bioconductor.org/browse/Pi/
Package Short Url https://bioconductor.org/packages/Pi/
Package Downloads Report Download Stats