Dmitry Grapov dgrapov
dgrapov
/ IDEOM small list
Last active
December 17, 2015 04:09
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| SMID Formula Metabolite Central Map Pathway KEGGpath KEGGid PubChem CID Lmid HMDBID MetacycID CHEBI METLIN InchiKEY Synonyms | |
| 11 H2O H2O Central Energy Metabolism Oxidative phosphorylation__Photosynthesis__Carbon fixation__Riboflavin metabolism map00190 C00001 962 HMDB02111 WATER 5585 3194 XLYOFNOQVPJJNP-UHFFFAOYSA-N Water | |
| 25361 C10H16N5O13P3 ATP Central Energy Metabolism Oxidative phosphorylation__Photosynthesis__Purine metabolism__Puromycin biosynthesis__Zeatin biosynthesis map00190 C00002 5957 HMDB00538 ATP 2359 95 ZKHQWZAMYRWXGA-KQYNXXCUSA-N Adenosine 5'-triphosphate | |
| 31698 C21H27N7O14P2 NAD+ Central Energy Metabolism Oxidative phosphorylation__Glutamate metabolism__Nicotinate and nicotinamide metabolism map00190 C00003 5893 HMDB00902 NAD 7422 101 BAWFJGJZGIEFAR-NNYOXOHSSA-O NAD_Nicotinamide adenine dinucleotide_DPN_Diphosphopyridine nucleotide_Nadide | |
| 31768 C21H29N7O14P2 NADH Central Energy Metabolism Oxidative phosphorylation map00190 C00004 439153 HMDB01487 NADH 7423 3687 BOPGDPNILDQYTO-NNYOXOHSSA-N D |
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| # R interface to Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH | |
| CIRgetR<-function(id,to=c("pubchem_sid"),return.all=TRUE,progress=TRUE){ | |
| #id needs to be one of the folowing types of structural ids "inchi","inchiKey" or "smiles" | |
| #to can be: smiles, names, iupac_name, cas, inchi, | |
| # stdinchi, inchikey, stdinchikey, | |
| # ficts, ficus, uuuuu, image, # here return url do not evaluate | |
| # mw, monoisotopic_mass,file, | |
| # chemspider_id | |
| # pubchem_sid, chemnavigator_sid, formula, chemnavigator_sid |
dgrapov
/ KEGG RPAIRS2.r
Last active
December 16, 2015 12:59
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| C00005 C00006 | |
| C00003 C00004 | |
| C00002 C00008 | |
| C00019 C00021 | |
| C00007 C00027 | |
| C00010 C00024 | |
| C00002 C00020 | |
| C00002 C00013 | |
| C00002 C00009 | |
| C00015 C00029 |
dgrapov
/ max intensity mass to charge pair.r
Created
April 4, 2013 21:52
Data processing script to get maximum m/z ion intensity pair from Agilent recursive analysis
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| #directory (file path) where the file is | |
| #note make sure all \ are changed to \\ or / | |
| dir<-"ZZZ" | |
| setwd(dir) # change directory | |
| #name of file, should be .csv | |
| file.name<-"XXX.csv" | |
| #load data into R this assumes there is a header | |
| input<-read.csv(file.name, header = TRUE) |
dgrapov
/ metabolomic network.R
Last active
December 15, 2015 18:49
Tutorial code for making edge lists for biochemical and chemical similarity networks
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| #load needed functions: R package in progress - "devium", which is stored on github | |
| source("http://pastebin.com/raw.php?i=Y0YYEBia") | |
| # get sample chemical identifiers here:https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=1 | |
| #Pubchem CIDs = cids | |
| cids # overview | |
| nrow(cids) # how many | |
| str(cids) # structure, wan't numeric | |
| cids<-as.numeric(as.character(unlist(cids))) # hack to break factor |
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| InChI=1S/C7H6O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,8-9H,(H,10,11) | |
| InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12) | |
| InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8) | |
| InChI=1S/C5H8O3/c1-3(2)4(6)5(7)8/h3H,1-2H3,(H,7,8) | |
| InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10) | |
| InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7) | |
| InChI=1S/C6H10O3/c1-4(2)3-5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9) | |
| InChI=1S/C6H8O5/c7-4(6(10)11)2-1-3-5(8)9/h1-3H2,(H,8,9)(H,10,11) | |
| InChI=1S/C7H6O4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H,(H,10,11) | |
| InChI=1S/C19H28O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-16,20H,4-11H2,1-2H3 |
dgrapov
/ CID to inChi Key
Last active
December 13, 2015 20:09
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| 19 GLDQAMYCGOIJDV-UHFFFAOYSA-N | |
| 36 RNQHMTFBUSSBJQ-UHFFFAOYSA-N | |
| 45 ROBFUDYVXSDBQM-UHFFFAOYSA-N | |
| 49 QHKABHOOEWYVLI-UHFFFAOYSA-N | |
| 51 KPGXRSRHYNQIFN-UHFFFAOYSA-N | |
| 58 TYEYBOSBBBHJIV-UHFFFAOYSA-N | |
| 70 BKAJNAXTPSGJCU-UHFFFAOYSA-N | |
| 71 FGSBNBBHOZHUBO-UHFFFAOYSA-N | |
| 72 YQUVCSBJEUQKSH-UHFFFAOYSA-N | |
| 76 FMGSKLZLMKYGDP-UHFFFAOYSA-N |
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| 689043 C01197 | |
| 6443013 C14762 | |
| 6443013 C14762 | |
| 6446027 C14765 | |
| 6446027 C14765 | |
| 11954058 C14813 | |
| 6439873 C16326 | |
| 6439873 C16326 | |
| 1004 C00009 | |
| 1023 C00013 |
dgrapov
/ KEGG reaction pairs
Last active
December 13, 2015 19:39
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| C00005 C00006 | |
| C00003 C00004 | |
| C00002 C00008 | |
| C00019 C00021 | |
| C00007 C00027 | |
| C00010 C00024 | |
| C00002 C00020 | |
| C00002 C00013 | |
| C00002 C00009 | |
| C00015 C00029 |
dgrapov
/ load devium.r
Last active
December 11, 2015 16:28
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| #load devium (or any other package) from github repo | |
| source.git.hub<-function(url = "https://github.com/dgrapov/devium/tree/master/R") | |
| { | |
| if(require(RCurl)==FALSE){install.packages("RCurl");library(RCurl)} else { library(RCurl)} | |
| #get the names of all scripts to source | |
| obj<-getURL("https://github.com/dgrapov/devium/tree/master/R",ssl.verifypeer=FALSE) | |
| tmp<-strsplit(obj,'href=\"/') | |
| tmp2<-unlist(strsplit(as.character(unlist(tmp)),'class')) | |
| scripts<-gsub("/blob","",gsub('\" ',"",tmp2[grep("dgrapov/devium/blob/master/R/",tmp2)])) # fix formatting |