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>
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 | ||
| NEWS | Text |
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) (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 | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.13 | Source Archive |