CNORfeeder
This is the released version of CNORfeeder; for the devel version, see CNORfeeder.
Integration of CellNOptR to add missing links
Bioconductor version: Release (3.23)
This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.
Author: Federica Eduati [aut, cre]
Maintainer: Attila Gabor <attila.gabor at uni-heidelberg.de>
citation("CNORfeeder")):
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("CNORfeeder")
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("CNORfeeder")| Main vignette:Playing with networks using CNORfeeder | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, NetworkInference, Proteomics, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0), graph |
| Imports | CellNOptR(>= 1.4.0) |
| System Requirements | |
| URL |
See More
| Suggests | minet, Rgraphviz, RUnit, BiocGenerics, igraph |
| Linking To | |
| Enhances | MEIGOR |
| 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 | CNORfeeder_1.52.0.tar.gz |
| Windows Binary (x86_64) | CNORfeeder_1.52.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CNORfeeder_1.52.0.tgz |
| macOS Binary (sonoma-arm64) | CNORfeeder_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNORfeeder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNORfeeder |
| Bioc Package Browser | https://code.bioconductor.org/browse/CNORfeeder/ |
| Package Short Url | https://bioconductor.org/packages/CNORfeeder/ |
| Package Downloads Report | Download Stats |