GAPGOM
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GAPGOM.
GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
Bioconductor version: 3.12
Collection of various measures and tools for lncRNA annotation prediction put inside a redistributable R package. The package contains two main algorithms; lncRNA2GOA and TopoICSim. lncRNA2GOA tries to annotate novel genes (in this specific case lncRNAs) by using various correlation/geometric scoring methods on correlated expression data. After correlating/scoring, the results are annotated and enriched. TopoICSim is a topologically based method, that compares gene similarity based on the topology of the GO DAG by information content (IC) between GO terms.
Author: Rezvan Ehsani [aut, cre], Casper van Mourik [aut], Finn Drabløs [aut]
Maintainer: Rezvan Ehsani <rezvanehsani74 at gmail.com>
citation("GAPGOM")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GAPGOM")
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("GAPGOM")| An Introduction to GAPGOM | HTML | R Script |
| Benchmarks and other GO similarity methods | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GO, GeneExpression, GenePrediction, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats |
| System Requirements | |
| URL | https://github.com/Berghopper/GAPGOM/ |
| Bug Reports | https://github.com/Berghopper/GAPGOM/issues/ |
See More
| Suggests | org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 |
| 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 | GAPGOM_1.6.0.tar.gz |
| Windows Binary | GAPGOM_1.6.0.zip |
| macOS 10.13 (High Sierra) | GAPGOM_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GAPGOM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GAPGOM |
| Bioc Package Browser | https://code.bioconductor.org/browse/GAPGOM/ |
| Package Short Url | https://bioconductor.org/packages/GAPGOM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |