rentrez | talk with NCBI entrez using R | Development Tools library

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 sequence data I want to retrieve, then creating a search that retrieves all the occurrences that match my query, and finally I create data where I retrieve the actual sequence data in fasta file.

Here is my html

I have a list of vectors, and I want to combine these, matched by ID, into a new data frame.

You can recreate my problem using this code:

I've been using the extremely useful rentrez package in R to get information about author, article ID and author affiliation from the Pubmed database. This works fine but now I would like to extract information from the affiliation field. Unfortunately the affiliation field is widely unstructured, not standardized string with various types of information such as the name of university, name of department, address and more delimited by commas. Therefore text mining approach is necessary to get any useful information from this field.

I tried the package easyPubmed in combination with rentrez, and even though easyPubmed package can extract some information from the affiliation field (e.g. email address, which is very useful), to my knowledge it cannot extract university name. I also tried the package pubmed.mineR, but unfortunately this also does not provide university name extraction. I startet to experiment with grep and regex functions but as I am no R expert I could not make this work.

I was able to find very similar threads solving the issue with python:

Regex for extracting names of colleges, universities, and institutes?

How to extract university/school/college name from string in python using regular expression?

But unfortunately I do not know how to convert the python regex function to an R regex function as I am not familiar with python.

Here is some example data:

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):

My method entreeIncorrecte is there to check for user input. If the value for ligne and colonne are anything other than "0", "1", "2" or "3", I want to print out that the user was incorrect and restart the loop for entreeIncorrecte. If I enter "e" and "3" for the row and column, the compiler gives me:

Exception in thread "main" java.lang.NumberFormatException: For input string: "e" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.base/java.lang.Integer.parseInt(Integer.java:652) at java.base/java.lang.Integer.parseInt(Integer.java:770) at td.Main.verifierEntree(Main.java:200) at td.Main.jouerUnePartie(Main.java:152) at td.Main.plusieursParties(Main.java:103) at td.Main.main(Main.java:32)

Is there anything to do about that?

N.B.: The code has to be written in French for my variables, methods, etc. by convention because of where I live, so sorry in advance for any confusion. Here is my code:

I'm having trouble creating a TicTacToe program for my class. It's a 4 x 4 board. My variables for my win condition method victoire() are giving me an error. The code has to be written in french for my variables, methods, etc. by convention because of where I live, so sorry in advance.

The errors are :

Multiple markers at this line - colonne2 cannot be resolved to a variable - ligne2 cannot be resolved to a variable

Lines 156 and 162 respectively

and the warnings are :

The value of the local variable colonne2 is not used

The value of the local variable ligne2 is not used

Lines 194 and 195 respectively

Here is my code :

I'm new to R and Shiny. So far I was able to make a script that fetches Protein sequences from ncbi with the rentrez package. However I can't manage to make it work in a shiny application.

I have following input in the ui

I am querying PubMED with a long list of PMIDs using R. Because entrez_fetch can only do a certain number at a time, I have broken down my ~2000 PMIDs into one list with several vectors (each about 500 in length). When I query PubMED, I am extracting information from XML files for each publication. What I would like to have in the end is something like this: