Pi

DOI: 10.18129/B9.bioc.Pi    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Pi.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

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

Details

biocViews	GeneExpression, GeneTarget, Genetics, GenomeWideAssociation, GraphAndNetwork, HiC, LinkageDisequilibrium, Network, Pathways, Software
Version	2.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (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
LinkingTo
Suggests	foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite
SystemRequirements
Enhances
URL	http://pi314.r-forge.r-project.org
BugReports	https://github.com/hfang-bristol/Pi/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Pi_2.4.0.tar.gz
Windows Binary	Pi_2.4.0.zip
macOS 10.13 (High Sierra)	Pi_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Pi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Pi
Package Short Url	https://bioconductor.org/packages/Pi/
Package Downloads Report	Download Stats