GAPGOM

This package is for version 3.13 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: 3.13

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 "4.1") 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 1.8.0
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_1.8.0.tar.gz
Windows Binary GAPGOM_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) GAPGOM_1.8.0.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 3.13 Source Archive