Package: GOxploreR 1.2.7

GOxploreR: Structural Exploration of the Gene Ontology (GO) Knowledge Base

It provides an effective, efficient, and fast way to explore the Gene Ontology (GO). Given a set of genes, the package contains functions to assess the GO and obtain the terms associated with the genes and the levels of the GO terms. The package provides functions for the three different GO ontology. We discussed the methods explicitly in the following article <doi:10.1038/s41598-020-73326-3>.

Authors:Kalifa Manjang, Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer

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GOxploreR.pdf |GOxploreR.html✨
GOxploreR/json (API)

# Install 'GOxploreR' in R:
install.packages('GOxploreR', repos = c('https://kalifa-manjang.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.15 score 1 stars 14 scripts 293 downloads 1 mentions 44 exports 99 dependencies

Last updated 1 years agofrom:74494779da. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:degreeDistBPdegreeDistCCdegreeDistMFdistRankingGOGene2GOTermAndLevelGene2GOTermAndLevel_ONGetDAGgetGOcategoryGetLeafNodesBPGetLeafNodesCCGetLeafNodesMFGO2DecBPGO2DecCCGO2DecMFGO4OrganismGOTermBP2ChildLevelGOTermBPOnLevelGOTermCC2ChildLevelGOTermCCOnLevelGOTermMF2ChildLevelGOTermMFOnLevelLevel2GOTermBPLevel2GOTermCCLevel2GOTermMFLevel2JumpNodeBPLevel2JumpNodeCCLevel2JumpNodeMFLevel2LeafNodeBPLevel2LeafNodeCCLevel2LeafNodeMFLevel2NoLeafNodeBPLevel2NoLeafNodeCCLevel2NoLeafNodeMFLevel2RegularNodeBPLevel2RegularNodeCCLevel2RegularNodeMFprioritizedGOTermsscoreRankingGOvisRDAGBPvisRDAGCCvisRDAGMFvisRsubDAGBPvisRsubDAGCCvisRsubDAGMF

Dependencies:annotateAnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicodacolorspacecpp11crayoncurlDBIdbplyrdigestdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataggforceggplot2ggraphggrepelglueGO.dbgontrgraphlayoutsgridExtragtablehmshttrhttr2igraphIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnetworknlmeopensslpillarpkgconfigplogrpngpolyclipprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangRSQLiteS4Vectorsscalesstatnet.commonstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXMLxml2xtableXVectorzlibbioc

Introduction to the GOxploreR package

Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer & Frank Emmert-Streib

Rendered fromGOxploreR.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-04-19
Started: 2020-11-20

Readme and manuals

Help Manual

Help pageTopics
Degree distribution of the GO biological process (BP) terms on a GO-leveldegreeDistBP
Degree distribution of the GO cellular component (CC) terms on a GO leveldegreeDistCC
Degree distribution of the GO molecular function (MF) terms on a GO-leveldegreeDistMF
Provides ranking of GO-terms according to distancedistRankingGO
Get the Gene Ontology (GO) terms associated with a gene(s) and their levelsGene2GOTermAndLevel
Get the Gene Ontology (GO) terms associated with a gene(s) and their levelsGene2GOTermAndLevel_ON
Organism-specific GO-DAG edgelistGetDAG
GO-term category gettergetGOcategory
All the BP GO-DAG leaf nodesGetLeafNodesBP
All the CC GO-DAG leaf nodesGetLeafNodesCC
All the MF GO-DAG leaf nodesGetLeafNodesMF
GO biological process (BP) descendant GO-terms as an EdgelistGO2DecBP
GO cellular component (CC) descendant GO-terms as an EdgelistGO2DecCC
GO molecular function (MF) descendant GO-terms as an EdgelistGO2DecMF
All gene association GO-terms for an organismGO4Organism
Get the level of a biological process (BP) GO term's childrenGOTermBP2ChildLevel
GO biological process (BP) terms level getterGOTermBPOnLevel
Get the level of a cellular component (CC) GO term's childrenGOTermCC2ChildLevel
GO cellular component (CC) terms level getterGOTermCCOnLevel
Get the level of a molecular function (MF) GO term's childrenGOTermMF2ChildLevel
GO molecular function (MF) term level getterGOTermMFOnLevel
GO biological process (BP) terms on a levelLevel2GOTermBP
GO cellular component (CC) terms on a levelLevel2GOTermCC
GO molecular function (MF) terms on a levelLevel2GOTermMF
Jump nodes from a GO BP levelLevel2JumpNodeBP
Jump nodes from a GO CC levelLevel2JumpNodeCC
Jump nodes from a GO MF levelLevel2JumpNodeMF
GO biological process (BP) level leaf nodes getterLevel2LeafNodeBP
GO cellular component (CC) level leaf nodes getterLevel2LeafNodeCC
GO molecular function (MF) level leaf nodes getterLevel2LeafNodeMF
Non-leaf GO-terms on a GO BP levelLevel2NoLeafNodeBP
Non-leaf GO-terms on a GO CC levelLevel2NoLeafNodeCC
Non-leaf GO-terms on a GO MF levelLevel2NoLeafNodeMF
Regular nodes from a GO BP levelLevel2RegularNodeBP
Regular nodes from a GO CC levelLevel2RegularNodeCC
Regular nodes from a GO MF levelLevel2RegularNodeMF
prioritization of a lists of GO-termsprioritizedGOTerms
Provides ranking of GO-terms according to a scorescoreRankingGO
Species-specific biological process GO-DAGvisRDAGBP
Species-specific cellular component GO-DAGvisRDAGCC
Species-specific molecular function GO-DAGvisRDAGMF
Visualise the GO-DAG for a specific organism based on certain GO-termsvisRsubDAGBP
Visualise the GO-DAG for a specific organism based on certain GO-termsvisRsubDAGCC
Visualise the GO-DAG for a specific organism based on certain GO-termsvisRsubDAGMF