Goseq
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Application data |
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| Created by | Young MD, Wakefield MJ, Oshlack A |
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| Biological application domain(s) | RNA-Seq quantification |
| Principal bioinformatics method(s) | Gene set testing |
| Technology | Illumina, ABI SOLiD |
| Created at | The Walter + Eliza Hall Institute |
| Maintained? | Yes |
| Programming language(s) | R |
| Licence | LGPL |
| Operating system(s) | UNIX, Windows |
Summary: An R package to detect Gene Ontology (GO) categories and other categories of genes (such as KEGG pathways) that are over/under represented in an RNA-seq data.
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The short read data produced by RNA-seq has the property that power to detect differential expression between samples is greater for longer transcripts than shorter ones. This gene length bias effects downstream tests that aim to determine if a given category of biological interest, such as one of the Gene Ontology categories, is over represented amongst DE genes.
The GOseq software package is designed to account for gene length bias by estimating the extent of this bias from the data. This information is incorporated into the statistical test for a categories over representation amongst DE genes. The resulting test is not biased by gene length.
In short, if you're testing for enrichment of a (GO) category in RNA-seq DE data, your results will be biased unless you take gene length into account. This package performs an unbiased test for category enrichment in RNA-seq DE data.
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