search for: entrez

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document but I have a prob...

I have used merge regularly and thought I understood how it worked, but I must not. I have two dataframes with identical colnames from two different experiments, TL01 and LC01. Each dataframe has a column named "Entrez.Gene", which I have converted to "as.character" just to make sure merge is not looking at factor levels. Because I have done some filtering, the Entrez.Gene values in each experiment overlap but are not identical. I want to produce a summary report with only those identifiers fou...

Dear all Does anybody know of updated Custom CDFs with binaries for MacOS. I'm trying to do affy-analysis using R-studio for Mac. Thanks Petter

...B Total 5874641 6295980 a 13 30 b 36 39 c 0 5 d 40 61 e 16 20 f 13 11 g 3 3 h 9 5 i 12 35 j 157 221 k 17 39 l 6 17 m 666 1387 n 2 5 The significance of digital gene expression profiles. Audic S <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C laverie%20JM%22%5BAuthor%5D&itool=EntrezSy...

...ut a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse(" http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ",isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities. Has anyone ever done...

Dear R folks: I am trying to use SSOAP (version 0.2-2) package in R (version 2.1.0,linux) to access SOAP service on NCBI (http://www.ncbi.nlm.nih.gov) its WSDL file is at http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <- genSOAPClientInterface(ncbi at operations[[1]], def = ncbi, ncbi at name, verbose=FALSE) > ff at functions$run_eInfo("db=pub...

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")), useInternalNodes=TRUE) I want to get the reply where BOTH the terms exist in abstract....

Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <- xmlTreeParse(getURL(paste(url,...

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

...he character "N/A"): "AB004048|MM8;NCBI Build 36|transcript|chr2|157251580|157253958|ExemplarFor 'AB004048'; gene_id '18111'; transcript_id 'AB004048'; gene_name 'Nnat'; alt '5730414I02Rik|AW107673|Peg5'; neuronatin|http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=18111" #obtain the exprs matrix for cluster analysis #ask questions DEG_files <- grep("bak", dir());#pay attention to the filenames exprs_files <- grep("copy", dir()); protein <- c(); assign_ex...

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only node 'pubdate' and its children, but I don't know how to do that u...

Hello, Have anybody made tools for g-estimation (introduced by J. Robins) in R. http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8235180&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Regards, Jari Haukka

Hello R community, I am processing raw Affymetrix CEL files and I am using the Michigan custom CDF library hgu133plus2hsentrezgprobe. I have been looking for documentation on the function that it contains...I am specifically interested in converting probe names to gene symbols. Does anybody know where I can find it? Thank a lot! Eleni [[alternative HTML version deleted]]

...O.db") library("AnnotationDbi") biocLite("org.At.tair.db") biocLite("ath1121501.db"). genenames <- org.At.tairGENENAME[ids] #map the probe ids to the gene names in TAIR The output of which is AnnDbBiMap[1] number<-org.At.tairENTREZID[ids] #map the probe ids to the gene ids in TAIR The output of which is AnnDbBiMap[1] And then I try to merge both the lists as : xx<-toTable(entrez) yy<-toTable(number) complete<-merge(xx,yy) I get an error in this step and unable to proceed further.The error r...

Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate, because I get the error: Error in file.exists(destfile) : object 'destfile' not found This is what I tried: UIDs<-esearch( "Methylation" ) accession_numbers

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

...ubDate") > print(node) > ) Gorjanc Gregor wrote: > Hello! > > I am trying to get specific fields from an XML document and I am totally > puzzled. I hope someone can help me. > > # URL > URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" > # download a XML file > tmp <- xmlTreeParse(URL, isURL = TRUE) > tmp <- xmlRoot(tmp) > > Now I want to extract only node 'pubdate' and its children, but I don'...