# Structural Exploration of the Gene Ontology (GO) Knowledge Base

## Documentation for package ‘GOxploreR’ version 1.2.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

degreeDistBP | Degree distribution of the GO biological process (BP) terms on a GO-level
degreeDistCC | Degree distribution of the GO cellular component (CC) terms on a GO level
degreeDistMF | Degree distribution of the GO molecular function (MF) terms on a GO-level
distRankingGO | Provides ranking of GO-terms according to distance
Gene2GOTermAndLevel | Get the Gene Ontology (GO) terms associated with a gene(s) and their levels
Gene2GOTermAndLevel_ON | Get the Gene Ontology (GO) terms associated with a gene(s) and their levels
GetDAG | Organism-specific GO-DAG edgelist
getGOcategory | GO-term category getter
GetLeafNodesBP | All the BP GO-DAG leaf nodes
GetLeafNodesCC | All the CC GO-DAG leaf nodes
GetLeafNodesMF | All the MF GO-DAG leaf nodes
GO2DecBP | GO biological process (BP) descendant GO-terms as an Edgelist
GO2DecCC | GO cellular component (CC) descendant GO-terms as an Edgelist
GO2DecMF | GO molecular function (MF) descendant GO-terms as an Edgelist
GO4Organism | All gene association GO-terms for an organism
GOTermBP2ChildLevel | Get the level of a biological process (BP) GO term's children
GOTermBPOnLevel | GO biological process (BP) terms level getter
GOTermCC2ChildLevel | Get the level of a cellular component (CC) GO term's children
GOTermCCOnLevel | GO cellular component (CC) terms level getter
GOTermMF2ChildLevel | Get the level of a molecular function (MF) GO term's children
GOTermMFOnLevel | GO molecular function (MF) term level getter
Level2GOTermBP | GO biological process (BP) terms on a level
Level2GOTermCC | GO cellular component (CC) terms on a level
Level2GOTermMF | GO molecular function (MF) terms on a level
Level2JumpNodeBP | Jump nodes from a GO BP level
Level2JumpNodeCC | Jump nodes from a GO CC level
Level2JumpNodeMF | Jump nodes from a GO MF level
Level2LeafNodeBP | GO biological process (BP) level leaf nodes getter
Level2LeafNodeCC | GO cellular component (CC) level leaf nodes getter
Level2LeafNodeMF | GO molecular function (MF) level leaf nodes getter
Level2NoLeafNodeBP | Non-leaf GO-terms on a GO BP level
Level2NoLeafNodeCC | Non-leaf GO-terms on a GO CC level
Level2NoLeafNodeMF | Non-leaf GO-terms on a GO MF level
Level2RegularNodeBP | Regular nodes from a GO BP level
Level2RegularNodeCC | Regular nodes from a GO CC level
Level2RegularNodeMF | Regular nodes from a GO MF level
prioritizedGOTerms | prioritization of a lists of GO-terms
scoreRankingGO | Provides ranking of GO-terms according to a score
visRDAGBP | Species-specific biological process GO-DAG
visRDAGCC | Species-specific cellular component GO-DAG
visRDAGMF | Species-specific molecular function GO-DAG
visRsubDAGBP | Visualise the GO-DAG for a specific organism based on certain GO-terms
visRsubDAGCC | Visualise the GO-DAG for a specific organism based on certain GO-terms
visRsubDAGMF | Visualise the GO-DAG for a specific organism based on certain GO-terms