Pi

This package is for version 3.14 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: 3.14

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 "4.1") and enter:


if (!require("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")

Pi User Manual (R/Bioconductor package) HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneTarget, Genetics, GenomeWideAssociation, GraphAndNetwork, HiC, LinkageDisequilibrium, Network, Pathways, Software

Version 2.6.0

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

Suggests foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite

Linking To

Enhances

Depends On Me

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Links To Me

Build Report Build Report

Package Archives

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

Source Package Pi_2.6.0.tar.gz

Windows Binary Pi_2.6.0.zip

macOS 10.13 (High Sierra) Pi_2.6.0.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

Old Source Packages for BioC 3.14 Source Archive