fgga
This is the released version of fgga; for the devel version, see fgga.
Hierarchical ensemble method based on factor graph
Bioconductor version: Release (3.23)
Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.
Author: Flavio Spetale [aut, cre]
Maintainer: Flavio Spetale <spetale at cifasis-conicet.gov.ar>
citation("fgga")):
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("fgga")
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("fgga")| FGGA: Factor Graph GO Annotation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GO, GraphAndNetwork, Network, NetworkInference, Software, StatisticalMethod, SupportVectorMachine |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.3), RBGL |
| Imports | graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph |
| System Requirements | |
| URL | https://github.com/fspetale/fgga |
See More
| Suggests | knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, 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 | fgga_1.20.0.tar.gz |
| Windows Binary (x86_64) | fgga_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | fgga_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | fgga_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fgga |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fgga |
| Bioc Package Browser | https://code.bioconductor.org/browse/fgga/ |
| Package Short Url | https://bioconductor.org/packages/fgga/ |
| Package Downloads Report | Download Stats |