PanViz

DOI: 10.18129/B9.bioc.PanViz    

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

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML R Script PanViz
PDF   Reference Manual

Details

biocViews GenomeWideAssociation, GraphAndNetwork, KEGG, Metabolomics, Network, Reactome, SNP, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo
Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3
SystemRequirements
Enhances
URL https://github.com/LucaAnholt/PanViz
BugReports https://github.com/LucaAnholt/PanViz/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 PanViz_1.0.0.tar.gz
Windows Binary PanViz_1.0.0.zip
macOS Binary (x86_64) PanViz_1.0.0.tgz
macOS Binary (arm64) PanViz_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PanViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PanViz
Package Short Url https://bioconductor.org/packages/PanViz/
Package Downloads Report Download Stats

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