topGO v2.24.0

by Adrian Alexa

Enrichment Analysis for Gene Ontology

topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Functions in topGO

Name Description
Gene set tests statistics Gene set tests statistics
classicCount-class Class "classicCount"
inducedGraph The subgraph induced by a set of nodes.
groupGOTerms Grouping of GO terms into the three ontologies
getSigGroups Interfaces for running the enrichment tests
classicExpr-class Class "classicExpr"
Determines the levels of a Directed Acyclic Graph (DAG) Utility functions to work with Directed Acyclic Graphs (DAG)
topGOdata-class Class "topGOdata"
geneList A toy example of a list of gene identifiers and the respective p-values
elimScore-class Classes "elimScore" and "weight01Score"
classicScore-class Class "classicScore"
printGraph-methods Visualisation functions
topGO-package Enrichment analysis for Gene Ontology
GOdata Sample topGOdata and topGOresult objects
dignostic-methods Diagnostic functions for topGOdata and topGOresult objects.
groupStats-class Class "groupStats"
elimCount-class Classes "elimCount" and "weight01Count"
parentChild-class Classes "parentChild" and "pC"
topGOresult-class Class "topGOresult"
getPvalues Convenient function to compute p-values from a gene expression matrix.
elimExpr-class Class "elimExpr"
annFUN Functions which map gene identifiers to GO terms
weightCount-class Class "weightCount"
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Details

Type Package
Date 2016-02-03
License LGPL
Collate AllClasses.R topGOmethods.R topGOgraph.R topGOalgo.R topGOfunctions.R topGOannotations.R topGOtests.R topGOviz.R zzz.R
biocViews Microarray, Visualization

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