topGO
topGO: Enrichment analysis for Gene Ontology
Bioconductor version: 2.9
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.
Author: Adrian Alexa, Jorg Rahnenfuhrer
Maintainer: Adrian Alexa <alexa at mpi-inf.mpg.de>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("topGO")
To cite this package in a publication, start R and enter:
citation("topGO")
Documentation
| R Script | topGO | |
| topGO_classes_v3.pdf | ||
| Reference Manual |
Details
| biocViews | Microarray, Bioinformatics, Visualization |
| Depends | R (>= 2.10.0), methods, graph(>= 1.14.0), Biobase(>= 2.0.0), GO.db(>= 2.3.0), AnnotationDbi(>= 1.7.19), SparseM (>= 0.73) |
| Imports | methods, graph, Biobase, SparseM, AnnotationDbi, lattice |
| Suggests | ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest |
| System Requirements | |
| License | LGPL |
| URL | |
| Depends On Me | RNAither |
| Imports Me | |
| Suggests Me | Ringo |
| Version | 2.6.0 |
| Since | Bioconductor 2.0 (R-2.5) |
Package Downloads
| Package Source | topGO_2.6.0.tar.gz |
| Windows Binary | topGO_2.6.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | topGO_2.6.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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