Pi

DOI: 10.18129/B9.bioc.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 (3.12)

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 at well.ox.ac.uk>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 2.1.0
In Bioconductor since BioC 3.4 (R-3.3) (3.5 years)
License GPL-3
Depends igraph, dnet, ggplot2, graphics
Imports Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice, caret, plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr, tidyr, ggnetwork, osfr, RCircos
LinkingTo
Suggests foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer
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_2.1.0.tar.gz
Windows Binary Pi_2.1.0.zip
macOS 10.13 (High Sierra) Pi_2.1.0.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

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