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GOxploreR (version 1.1.0)

Structural Exploration of the Gene Ontology (GO) Knowledge Base

Description

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 .

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Version

Install

install.packages('GOxploreR')

Monthly Downloads

151

Version

1.1.0

License

GPL-2

Maintainer

Kalifa Manjang

Last Published

November 20th, 2020

Functions in GOxploreR (1.1.0)

GO2DecBP

GO biological process (BP) descendant GO-terms as an Edgelist
GOTermMFOnLevel

GO molecular function (MF) term level getter
GOTermBPOnLevel

GO biological process (BP) terms level getter
GO2DecCC

GO cellular component (CC) descendant GO-terms as an Edgelist
GOTermBP2ChildLevel

Get the level of a biological process (BP) GO term's children
GOTermMF2ChildLevel

Get the level of a molecular function (MF) GO term's children
GO2DecMF

GO molecular function (MF) descendant GO-terms as an Edgelist
GOTermCCOnLevel

GO cellular component (CC) terms level getter
GOTermsApp.M

Title
GetLeafNodesBP

All the BP GO-DAG leaf nodes
Level2LeafNodeCC

GO cellular component (CC) level leaf nodes getter
GetLeafNodesMF

All the MF GO-DAG leaf nodes
visRsubDAGCC

Visualise the GO-DAG for a specific organism based on certain GO-terms
degreeDistCC

Degree distribution of the GO cellular component (CC) terms on a GO level
Gene2GOTermAndLevel

Get the Gene Ontology (GO) terms associated with a gene(s) and their levels
degreeDistMF

Degree distribution of the GO molecular function (MF) terms on a GO-level
visRsubDAGMF

Visualise the GO-DAG for a specific organism based on certain GO-terms
Level2JumpNodeBP

Jump nodes from a GO BP level
distRankingGO

Provides ranking of GO-terms according to distance
Level2GOTermBP

GO biological process (BP) terms on a level
Level2JumpNodeCC

Jump nodes from a GO CC level
GO4Organism

All gene association GO-terms for an organism
Gene2GOTermAndLevel_ON

Get the Gene Ontology (GO) terms associated with a gene(s) and their levels
maxLevelBP

Return length of depth for bp
visRDAGCC

Species-specific cellular component GO-DAG
visRDAGBP

Species-specific biological process GO-DAG
Level2NoLeafNodeBP

Non-leaf GO-terms on a GO BP level
GetLeafNodesCC

All the CC GO-DAG leaf nodes
Level2NoLeafNodeMF

Non-leaf GO-terms on a GO MF level
Level2NoLeafNodeCC

Non-leaf GO-terms on a GO CC level
goterm.org

Title
drawGraph

Visualize GO DAG
GetDAG

Organism-specific GO-DAG edgelist
Level2LeafNodeMF

GO molecular function (MF) level leaf nodes getter
Level2LeafNodeBP

GO biological process (BP) level leaf nodes getter
Level2JumpNodeMF

Jump nodes from a GO MF level
Level2RegularNodeBP

Regular nodes from a GO BP level
getNodeTerms

Retrieve GO terms in each category
getGOcategory

GO-term category getter
visRsubDAGBP

Visualise the GO-DAG for a specific organism based on certain GO-terms
visRDAGMF

Species-specific molecular function GO-DAG
maxLevelCC

Return length of depth for cc
Level2RegularNodeMF

Regular nodes from a GO MF level
Level2RegularNodeCC

Regular nodes from a GO CC level
maxLevelMF

Return length of depth for mf
GOTermsApp.B

Building tree one
edgelistCC

Title
edgelistMF

Title
scoreRankingGO

Provides ranking of GO-terms according to a score
prioritizedGOTerms

prioritization of a lists of GO-terms
GOTermsApp.C

Title
Level2GOTermMF

GO molecular function (MF) terms on a level
Level2GOTermCC

GO cellular component (CC) terms on a level
degreeDistBP

Degree distribution of the GO biological process (BP) terms on a GO-level
all_terms_level_h2

Building tree
drawGraph4Vis

Visualize GO DAG
edgelistBP

Title
GOTermCC2ChildLevel

Get the level of a cellular component (CC) GO term's children