Stack Overflow
Stack Overflow

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.

38 questions
0
votes
0 answers

How do I BLAST in R, Extract species names from NCBI taxonomy data using rentrez in R?

I am a student working on a microbiome project and I am using R to retrieve species names from NCBI taxonomy data. I have obtained the accession numbers through rBLAST and now I need to retrieve the corresponding species names. I have tried using…
Chiara
  • 1
0
votes
0 answers

Why does my pattern extractor code return false positives?

My goal was to extract the sequence of "Antimicrobial Peptides" from the NCBI Database using keywords such as "Antimicrobial Peptides, AMPs" and also specifying its length. I have written a code to extract the sequences of Antimicrobial Peptides…
Abdullah Afzal
  • 1
0
votes
1 answer

Why does my for loop in Python never stop running?

I am creating a code that takes accession numbers from an existing excel file and ultimately running it through BLAST using Entrez. I am very new to Python and pretty much just learning as a I write. Here is what my code looks like right now, it…
Brianna Nissley
  • 1
0
votes
0 answers

NCBI Rentrez timeout HTTP failure 400

I am running a loop through Biosample IDs to store their metadata in a dataframe for about 15,000 IDs. I have the formatting for how I want to retrieve and store the XML data into an R dataframe but each time that I try to run the loop it times out…
Dylan Stephens
  • 1
0
votes
1 answer

Downloading DNA sequence data in R using entrez_fetch: cannot retrieve query

I'm trying to download DNA sequence data from NCBI using entrez_fetch. With the following code, I perform a search for the IDs of the sequences I need with entrez_search, and then I attempt to download the sequence data in FASTA…
notasfarwest
  • 71
  • 5
0
votes
1 answer

Extracting author and affiliation from xml file retrieved using rentrez

I was following this post's code: https://quantixed.org/2021/04/04/ten-years-vs-the-spread-ii-calculating-publication-lag-times-in-r/ and was amazed at the ability to output received, accepted and published dates/gaps between them. Would there be a…
mickmars51
  • 1
  • 2
0
votes
0 answers

Rentrez not accepting quote escaping

I'm using R rentrez package to retrieve pubmed information. In general, when pubmed interpreter detects a compound phrase, it automatically adds quotation in order to include searching for exact phrase. Nevertheless, this doesn't happens every time,…
panchtox
  • 634
  • 7
  • 16
0
votes
1 answer

using pubmedR to search by doi

trying to use the methods here and here to extract author affiliation from a list of doi's but not finding any info out there on using pubmedR to search by doi. have looked into entrez syntax but no luck there also. please help! thank you
tataṣe
  • 49
  • 6
0
votes
1 answer

How do I provide my Identity / Email when connecting to NCBI through Rentrez?

My project head is telling me that its unacceptable to connect with NCBI to retrieve sequence entries without sending along identifying information such as our institution email. They claim this means NCBI won't instantly block our connection if we…
BioInfoMan28
  • 1
0
votes
2 answers

Using R to fetch a Pubmed abstract by using its title

I have been trying for a while to fetch Pubmed abstracts by using its title. For istance, if I put the following title on the pubmPd mask @ https://pubmed.ncbi.nlm.nih.gov/ : A Pituitary-Derived MEG3 Isoform Functions as a Growth Suppressor in Tumor…
Arturo
  • 342
  • 1
  • 4
  • 14
0
votes
1 answer

How to retrieve data using the rentrez package by giving a list of query names instead of a single one?

So I'm trying to use the rentrez package to retrieve DNA sequence data from GenBank, giving as input a list of species. What I've done is create a vector for the species I want to query, followed by creating a term where I specify the types of…
tadeufontes
  • 443
  • 1
  • 3
  • 12
0
votes
2 answers

Is it possible to get the number of times an article has been cited?

I am using Entrez to search for articles on Pubmed. Is it possible to use Entrez to also determine the number of citations for each article that is found using my search parameters? If not, is there an alternative method that I can use? My…
user70711
  • 131
  • 1
  • 9
0
votes
1 answer

Data.frame two list, each list contain different length of elements

I have a data frame with two lists of variables. Each observation in the list contains different length of elements. For example the 4th of the variable “accession” contains one element but 7th contains two elements. current dataframe I want to…
R beginnnnnner
  • 11
  • 5
0
votes
0 answers

Request limit and lapply

I want to make thousands of entrez requests. I know that you are not allowed to make more than 3 requests per second unless you have an API key. The rentrez introduction says that rentrez enforces this limit. I just want to make sure that NCBI does…
Martin Graßhoff
  • 65
  • 5
0
votes
1 answer

Parsing xml from a NCBI entrez in R

I want to extract some informations from the features section of a NCBI entry and I'm using this code. To download the data fetch2 <- entrez_fetch(db = "nucleotide", id = 1028916732, rettype = "gbc", retmode="xml", parsed =…
Eduardo
  • 7
  • 4
1
2
3