Path2PPI
This is the released version of Path2PPI; for the devel version, see Path2PPI.
Prediction of pathway-related protein-protein interaction networks
Bioconductor version: Release (3.23)
Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.
Author: Oliver Philipp [aut, cre], Ina Koch [ctb]
Maintainer: Oliver Philipp <contact at oliverphilipp.info>
citation("Path2PPI")):
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")
BiocManager::install("Path2PPI")
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("Path2PPI")| Path2PPI - A brief tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Network, NetworkInference, Pathways, Proteomics, Software, SystemsBiology |
| Version | 1.42.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.2.1), igraph (>= 1.0.1), methods |
| Imports | |
| System Requirements | |
| URL | http://www.bioinformatik.uni-frankfurt.de/ |
See More
| Suggests | knitr, rmarkdown, RUnit, BiocGenerics, 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 | Path2PPI_1.42.0.tar.gz |
| Windows Binary (x86_64) | Path2PPI_1.42.0.zip |
| macOS Binary (big-sur-x86_64) | Path2PPI_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | Path2PPI_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Path2PPI |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Path2PPI |
| Bioc Package Browser | https://code.bioconductor.org/browse/Path2PPI/ |
| Package Short Url | https://bioconductor.org/packages/Path2PPI/ |
| Package Downloads Report | Download Stats |