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Questions tagged [rentrez]

Provides an R interface to the NCBI's EUtils API allowing users to search databases like GenBank and PubMed, process the results of those searches and pull data into their R sessions.

Provides an R interface to the NCBI's EUtils API allowing users to search databases like GenBank and PubMed, process the results of those searches and pull data into their R sessions.

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Lists of summaries from rentrez stop working after being merged using append()

tl;dr: What is different about an esummary list produced by rentrez, and why do said lists stop working with other rentrez functions after they are merged using append()? I am accessing Pubmed using rentrez. I am able to search for publications and…
Josh
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rentrez error HTTP failure: 400 when downloading >1/3 of records

I have a weird situation. I am mining PubMed data using rentrez. When I run entrez_search() and then entrez_summary() and then entrez_fetch() I get the message this error (full code at the bottom of post): Error: HTTP failure: 400
Josh
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Vectorizing for-loop in R

Oh, man. I am so terrible at removing for-loops from my code because I find them so intuitive and I first learned C++. Below, I am fetching IDs for a search (copd in this case) and using that ID to retrieve its full XML file and from that save its…
sweetmusicality
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Scrape data from PubMed

I have written the following function to extract data from PubMed using Entrez: def getFromPubMed(id): handle = Entrez.efetch(db="pubmed",rettype="medline",retmode="text", id=str(id)) records = Medline.parse(handle) for record in…
jdoe
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Differences between Biopython NCBI/Entrez esummary output and R package output

I am new to accessing Entrez through Biopython and a couple of R packages (rentrez and reutil). When accessing the 'nuccore' database with esummary, the output fields returned by Biopython are different than that returned by the R packages.…
vethno
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Storing data in data frame from for loop - rentrez

I'm trying to find a list of SNPs that have PubMed entries using the rentrez package. When I run the code below, I end up with a NULL data frame. I think I'm not writing the data frame correctly. library(rentrez) term <- c('AKR1C1[GENE] AND…
JoeShmo
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Unable to use RCurl in R on Windows

I have installed curl from this weblink. I have my system path also updated with curl install directory and I am able to curl from the command prompt. I have also installed RCurl. But, my RStudio throws this error: Error in loadNamespace(name) :…
MD Naseem Ashraf
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How to ignore comma in text para when saving in .csv format?

I am trying to extract data from NCBI using different functions in rentrez package. However, I have an issue because the function extract_from_esummary() in rentrez results in matrix, where text of a column is splitted into adjacent columns when…
user5249203
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