PanViz

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

Bioconductor version: Release (3.19)

This pacakge integrates data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with summary-level genome-wide association (GWAS) data, such as that provided by the GWAS Catalog or GWAS Central databases, or a user's own study or dataset, in order to produce biological networks, termed IMONs (Integrated Multi-Omic Networks). IMONs can be used to analyse trait-specific polymorphic data within the context of biochemical and metabolic reaction networks, providing greater biological interpretability for GWAS data.

Author: Luca Anholt [cre, aut]

Maintainer: Luca Anholt <la1317 at ic.ac.uk>

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

Installation

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


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

BiocManager::install("PanViz")

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("PanViz")

PanViz	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomeWideAssociation, GraphAndNetwork, KEGG, Metabolomics, Network, Reactome, SNP, Software
Version	1.6.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	tidyr, stringr, dplyr, tibble, magrittr, futile.logger, utils, easycsv, rentrez, igraph, RColorBrewer, data.table, colorspace, grDevices, rlang, methods
System Requirements
URL	https://github.com/LucaAnholt/PanViz
Bug Reports	https://github.com/LucaAnholt/PanViz/issues

Suggests	testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	PanViz_1.6.0.tar.gz
Windows Binary (x86_64)	PanViz_1.6.0.zip (64-bit only)
macOS Binary (x86_64)	PanViz_1.6.0.tgz
macOS Binary (arm64)	PanViz_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PanViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PanViz
Bioc Package Browser	https://code.bioconductor.org/browse/PanViz/
Package Short Url	https://bioconductor.org/packages/PanViz/
Package Downloads Report	Download Stats