GAPGOM

DOI: 10.18129/B9.bioc.GAPGOM    

This is the development version of GAPGOM; to use it, please install the devel version of Bioconductor.

GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Bioconductor version: Development (3.9)

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: Casper Peters [aut, cre], Finn Drabløs [aut], Rezvan Ehsani [aut]

Maintainer: Casper Peters <cp100u at hotmail.com>

Citation (from within R, enter citation("GAPGOM")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GAPGOM", version = "3.9")

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")

 

HTML R Script An Introduction to GAPGOM
HTML R Script Benchmarks and other GO similarity methods
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GO, GeneExpression, GenePrediction, Software
Version 0.99.33
License MIT + file LICENSE
Depends R (>= 3.6.0)
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
LinkingTo
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
SystemRequirements
Enhances
URL https://github.com/Berghopper/GAPGOM/
BugReports https://github.com/Berghopper/GAPGOM/issues/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GAPGOM_0.99.33.tar.gz
Windows Binary GAPGOM_0.99.33.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GAPGOM_0.99.33.tgz
Source Repository git clone https://git.bioconductor.org/packages/GAPGOM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GAPGOM
Package Short Url http://bioconductor.org/packages/GAPGOM/
Package Downloads Report Download Stats

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