PanViz
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of PanViz; for the stable release version, see PanViz.
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
Bioconductor version: Development (3.21)
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("PanViz")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("PanViz")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GenomeWideAssociation, GraphAndNetwork, KEGG, Metabolomics, Network, Reactome, SNP, Software |
| Version | 1.9.1 |
| 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 |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3 |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |