Comments (3)
sckott
commented on July 2, 2024
any ideas here @DomBennett ?
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DomBennett
commented on July 2, 2024
Hi @sckott,
Yup, sequences!
The package acts as a portal to NCBI GenBank, which, as of August 2019, hosts some 213,865,349 sequences. But the package likely also makes use of the WGS information too as it will pull out any relevant annotated sequence. So maybe you're best data metric is number of bases: 366,733,917,629 + 5,585,922,333,160 = ~6e+12
For the most part, the phylotaR package uses the rentrez package. So whatever stats you pull up for that package, with respect to GenBank, applies to this one too.
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sckott
commented on July 2, 2024
thanks for this! David did give me some numbers for rentrez, but that bases estimate is a nice one he didn't have.
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Related Issues (20)
- problem with the restez/phylota integration
- Possibility to supply NCBI API key when running pipeline to access NCBI data faster? HOT 1
- Use phylotaR for retrieving orthologous protein sequences HOT 1
- No periods or tildes in file paths HOT 3
- Multiple markers/loci per cluster issue HOT 4
- Can not install the package in windows HOT 2
- Clusters with different parent number but the same MAD, seed, length, n_taxa, n_seqs
- Description - not enough information
- New Maintainer Wanted HOT 5
- Next release HOT 6
- CRAN archive of package outsider
- Fix pkgdown configuration for reference HOT 3
- No need for restez_connect() HOT 1
- Remove treeman as a dependency? HOT 2
- Could get something new from https://github.com/pachterlab/gget
- test failure HOT 1
- Generating taxonomic dictionary error HOT 1
- Fetch and error seem to be stuck HOT 2
- drop taxa functionality HOT 1
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