rentrez

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Bisaloo

When `api_key` is not provided, Entrez allows 3 requests per second, thus `sleep_time` should be at least (1/3) second. Rounding error caused it to wait for less than (1/3), resulting...

ttdtrang

Feature Request: Enable an update method for entrez_search

1

Thank you for the `rentrez` package! I'm currently using it to assist with a meta-analysis. Within that, I need to be able to track why articles are not included in...

billdenney

entrez_link by_id = TRUE with web_history

2

Right now it appears you can only use `by_id = TRUE` if you are supplying IDs with `id`, but it would be great if it also worked when a `web_history`...

willgearty

Question about entrez_link function

6

hey @dwinter - tried to figure this out, but you can probably do so much faster. Question from twitter https://twitter.com/neilfws/status/461109878262493184 `entrez_link(dbfrom="pccompound",db="all",id="62857")` gives no results from db "gds" But `db="gds"` (`entrez_link(dbfrom="pccompound",db="gds",id="62857")`)...

sckott

some more e-utility code

1

David, I just posted some code from my genomes package to connect to NCBI - its similar to what you have been working on so I thought it might be...

cstubben

Using web history instead of ids returns more results than expected

5

When I run `entrez_search()` with `use_history` and `retmax = 5`, the function will respect this and return 5 UIDs: ``` biosample_uid

stitam

For the past week I have tried to download coding sequences from the NCBI Reference Sequence: NC_000913.3. However given the fact that no transcript sequences are listed for this sequence,...

valkm2

multiple check_xml_errors when using entrez_link of protien IDs of Metagenomic assembled genomes from NCBI

2

When I run the following I get the results I am looking for: entrez_link(db="taxonomy", dbfrom="protein", id=c("QNO56202.1","RCV65969.1","OYV13592.1", "WP_138323301.1","WP_007546357.1","KPJ68349.1", "RLB10506.1"), by_id=TRUE) However, if I run any protein id of a MAG thats...

TJrogers86

Institution/organization info via rentrez

4

Good day! A GenBank info page contains data on the organization made sequencing. Can it be extracted via rentrez *not downloading* an entire gb file with `db="nuccore"`, `rettype = "gb"`?...

trilisser