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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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) | MetaPathNet_0.99.5.tgz |
| 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 |