MetaPathNet
This is the development version of MetaPathNet; to use it, please install the devel version of Bioconductor.
KEGG-Based Metabolic and Signaling Network Analysis for Systems Biology
Bioconductor version: Development (3.24)
Provides tools to construct KEGG-based metabolic and signaling networks as edge lists for single-organism or cross-species analyses. The package supports identifier mapping, shortest-path and topology analyses, community detection, permutation testing, pathway over-representation analysis, and node annotation for host-microbiome studies. It also provides network visualisation in R and Cytoscape and supports extension of KEGG-based networks through additional reaction resources and user-defined reactions.
Author: Zhaojie Wang [aut, cre]
, Francesc Puig-Castellvi [aut], Manyi Jia [aut], Marc-Emmanuel Dumas [aut, ths], Centre National de la Recherche Scientifique [fnd], Imperial College London [fnd], French National Research Agency [fnd]
Maintainer: Zhaojie Wang <zhaojie.wang at cnrs.fr>
citation("MetaPathNet")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MetaPathNet")
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("MetaPathNet")| MetaPathNet: network analysis of the choline-TMA-TMAO host-microbiome axis | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, KEGG, Microbiome, Network, Pathways, Software, SystemsBiology |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | igraph, httr, utils, RCurl, RCy3, tidygraph, ggraph, dplyr, KEGGREST, KEGGgraph, graph, mygene, ggplot2, rlang, curl, jsonlite, webchem, grDevices, grid, stats |
| System Requirements | Cytoscape (>= 3.9.0) for Cytoscape-based visualisation functions |
| URL | https://github.com/zhaojie-wang/MetaPathNet |
| Bug Reports | https://github.com/zhaojie-wang/MetaPathNet/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle |
| 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 | MetaPathNet_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MetaPathNet_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaPathNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaPathNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetaPathNet/ |
| Package Short Url | https://bioconductor.org/packages/MetaPathNet/ |
| Package Downloads Report | Download Stats |