User: omarrafiqued

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omarrafiqued50
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Posts by omarrafiqued

<prev • 9 results • page 1 of 1 • next >
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Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
... KEGG is a database resource (http://www.genome.jp/kegg/) that contains all information of genomes, their relationships to biological systems and their interactions with the environment. We use KEGG pathway database to identify the main functional and metabolic pathways in deferentially expresse ...
R kegg offline pathway enrichment written 7 weeks ago by omarrafiqued50
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Querying CTD database to find diseases associated with the given pathways.
... I need all the diseases associated with the given pathways. The CTD database is to be queried to check if the over-represented pathways are known to be associated to the disease. The association between a disease and a pathway is inferred by the number of genes that the pathway shares with those a ...
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Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
... For the following code, when there is no internet connection, I get the error "Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... function (species) { keggpathid2extid.df <- kegg_link(spe ...
pathview kegg gene mapping written 10 weeks ago by omarrafiqued50
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Comment: C: Mapping of GENE symbols into ENTREZ
... Thanks for the elaborate answer. ...
written 10 weeks ago by omarrafiqued50
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Comment: C: Mapping of GENE symbols into ENTREZ
... This is very useful. Thanks. ...
written 10 weeks ago by omarrafiqued50
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Comment: C: Mapping of GENE symbols into ENTREZ
... Yea, it is the trailing digits. Thanks for the code. I wrote my own code too: f1 <- function(x) { ENTIDS <- c() for(fa in x){ si<-str_length(fa) #str_sub(fa,-4,-4) ent1<-c() for (k in seq(1:si)){ ss=str_sub(fa,-k,-k) nl< ...
written 10 weeks ago by omarrafiqued50
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Comment: C: Mapping of GENE symbols into ENTREZ
... I got it. The last four numbers n each entry are the ENTREZIDs.... Took me time as I have no expertise in this area. ...
written 10 weeks ago by omarrafiqued50
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Comment: C: Mapping of GENE symbols into ENTREZ
... Thanks and yes. I figured that out just now. Do you have any idea how to extract the Gene Symbols???? e.g. for "UNKLLLL64718" , "UNK" is a Gene Symbol , but I cant find a pattern. ...
written 10 weeks ago by omarrafiqued50
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Mapping of GENE symbols into ENTREZ
... Below GG is the list of gene symbols to be mapped into entrez. The code is: geneMapping2= select(org.Hs.eg.db, GG, c("ENTREZID","GENENAME"),"ALIAS") The error is: Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ALIAS'. Please use t ...
annotation limma gene written 10 weeks ago by omarrafiqued50 • updated 10 weeks ago by Gordon Smyth39k

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