SemDist
This is the development version of SemDist; for the stable release version, see SemDist.
Information Accretion-based Function Predictor Evaluation
Bioconductor version: Development (3.24)
This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.
Author: Ian Gonzalez and Wyatt Clark
Maintainer: Ian Gonzalez <gonzalez.isv at gmail.com>
citation("SemDist")):
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("SemDist")
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("SemDist")| introduction.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Classification, GO, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.1), AnnotationDbi, GO.db, annotate |
| Imports | |
| System Requirements | |
| URL | http://github.com/iangonzalez/SemDist |
See More
| Suggests | GOSemSim |
| 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 | SemDist_1.47.0.tar.gz |
| Windows Binary (x86_64) | SemDist_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | SemDist_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | SemDist_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SemDist |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SemDist |
| Bioc Package Browser | https://code.bioconductor.org/browse/SemDist/ |
| Package Short Url | https://bioconductor.org/packages/SemDist/ |
| Package Downloads Report | Download Stats |