Package: GAPGOM
Type: Package
Title: GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
Version: 1.6.0
Authors@R: c(
    person("Rezvan", "Ehsani", email = "rezvanehsani74@gmail.com", role = c("aut", "cre")),
	person("Casper", "van Mourik", email = "cp100u@hotmail.com", role = "aut"),
    person("Finn", "Drabløs", email = "finn.drablos@ntnu.no", role = "aut"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
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
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
Depends: R (>= 4.0)
biocViews: GO, GeneExpression, GenePrediction
BugReports: https://github.com/Berghopper/GAPGOM/issues/
URL: https://github.com/Berghopper/GAPGOM/
RoxygenNote: 6.1.1
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GAPGOM
git_branch: RELEASE_3_12
git_last_commit: 48b8298
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
NeedsCompilation: no
Packaged: 2020-10-28 00:17:35 UTC; biocbuild
Author: Rezvan Ehsani [aut, cre],
  Casper van Mourik [aut],
  Finn Drabløs [aut]
Maintainer: Rezvan Ehsani <rezvanehsani74@gmail.com>
Built: R 4.0.3; ; 2021-03-29 21:18:56 UTC; unix
