README.md

In wilsontom/hmdbR: Search the Human Metabolome Database (HMDB) from the R console

hmdbR

search the Human Metabolome Database from the R Console

Useage

devtools::install_github("wilsontom/hmdbR")

library(hmdbR)

results <- search_hmdb("anserine")

dim(results)
[1] 3 7

results[,"name"]
[1] "Anserine"     "Homoanserine" "Mianserin"  


results[,c("name", "smiles", "accession_id")]
             name                               smiles accession_id
126      Anserine    CN1C=NC=C1C[C@H](NC(=O)CCN)C(O)=O    HMDB00194
2541 Homoanserine   CN1C=NC=C1C[C@H](NC(=O)CCCN)C(O)=O    HMDB05767
9876    Mianserin CN1CCN2C(C1)C1=CC=CC=C1CC1=CC=CC=C21    HMDB15620

References

Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35 (Database issue):D521-6. 17202168

Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 37(Database issue):D603-610. 18953024

Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7. 23161693

wilsontom/hmdbR documentation built on May 4, 2019, 6:29 a.m.