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 (3.10)

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>

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


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

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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


biocViews GO, GeneExpression, GenePrediction, Software
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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,,, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats
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