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freesci/gist:5240374

Created March 25, 2013 20:24
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Creating an annotation database in Bioconductor for non-model organism
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gistfile1.r
source("http://bioconductor.org/biocLite.R")
library(AnnotationForge)
makeOrgPackageFromNCBI(version="0.0.1",author="PS",maintainer="PS <ps@pawelszczesny.org>",outputDir=".",tax_id=4081,genus="Solanum", species="lycopersicum")
#here you need to wait a bit, few hours maybe
install.packages("org.Slycopersicum.eg.db", repos=NULL, type="source")
library("org.Slycopersicum.eg.db/")
keys<-head(keys(org.Slycopersicum.eg.db))
head(select(org.Slycopersicum.eg.db, keys=keys,cols=c("ENTREZID","ACCNUM","ALIAS","CHR","PMID","REFSEQ","SYMBOL","UNIGENE" ,"GENENAME"))
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