CLEAN.Mm-package | R Documentation |
Provide functional specific to Mus musculus to the CLEAN package. GO : Gene Ontolgy categories derived from packages GO.db and org.Mm.eg.db chrLoc: Cytogenetic bands, derived from the org.Mm.eg.db package geneRIFs: Keyword based text search of cancer related gene RIFs. Derived from NCBI gene RIFs (Gene Reference Into Function, websites: http://www.ncbi.nlm.nih.gov/projects/GeneRIF/ and ftp://ftp.ncbi.nih.gov/gene/GeneRIF/) GSEA : Gene Set Enrichment Analysis; categories compiled by the Broad Institute (website: http://www.broad.mit.edu/gsea/index.jsp, reference: Subramanian et al. (2005) ; Mootha, et al. (2003)) KEGG : Kyoto Encyclopedia of Genes and Genomes (KEGG) derived from the KEGG.db package. MP : Mouse phenotype (reference: Bult et al. (2008); website: http://www.informatics.jax.org/) CTD : Comparative Toxicogenomics Database transfac : Transfac derived categories.
Package: | CLEAN.Mm |
Type: | Package |
Version: | 1.0.0 |
Date: | 2009-03-30 |
License: | GPL>=2 |
LazyLoad: | yes |
Use CLEAN.Mm() to display available category types.
Johannes Freudenberg, Mario Medvedovic
Maintainer: Mario Medvedovic <Mario.Medvedovic@uc.edu>
Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273) Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA; and the members of the Mouse Genome Database Group. 2008. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36(Database issue):D724-8.
CLEAN
library(CLEAN) CLEAN.Mm() functionalCategories <- getFunctionalCategories(CLEAN.Mm(), species = "Mm") ### not run #library(CLEAN) #data(gimmOut) #runCEAN(gimmOut, functionalCategories = getFunctionalCategories(CLEAN.Mm(), species = "Mm"))
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