DOI: 10.18129/B9.bioc.GAPGOM  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GAPGOM.

GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Bioconductor version: 3.16

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>

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


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biocViews GO, GeneExpression, GenePrediction, Software
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 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,,, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats
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