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 (from within R, enter 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 PDF
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
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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