How can I download all supported species information table of STRINGdb V11
0
Entering edit mode
Evan-GIBH • 0
@user-24198
Last seen 3 days ago

Hello, Is it possible to download all STRINGdb V11 supported species information as a CSV/TSV table? I noticed that there is a function (get_STRING_species) in the older version that can do that work, and it only can download the species for version 10. So how can I download the species information for version 11? Thanks to anyone who can support help!

STRINGdb STRING • 52 views
ADD COMMENTlink
0
Entering edit mode
@Vincent-J.-Carey,-Jr.-4
Last seen 1 day ago
United States
> library(readr)
1/7 packages newly attached/loaded, see sessionInfo() for details.
> z = read_tsv("https://stringdb-static.org/download/species.v11.0.txt")

── Column specification ────────────────────────────────────────────────────────────────────────────────────────
cols(
  `## taxon_id` = col_double(),
  STRING_type = col_character(),
  STRING_name_compact = col_character(),
  official_name_NCBI = col_character()
)

> z[1:5,]
# A tibble: 5 x 4
  `## taxon_id` STRING_type STRING_name_compact       official_name_NCBI        
          <dbl> <chr>       <chr>                     <chr>                     
1           287 core        Pseudomonas aeruginosa    Pseudomonas aeruginosa    
2           292 core        Burkholderia cepacia      Burkholderia cepacia      
3           301 core        Pseudomonas oleovorans    Pseudomonas oleovorans    
4           340 core        Xanthomonas campestris c… Xanthomonas campestris pv…
5           359 core        Agrobacterium rhizogenes  Agrobacterium rhizogenes  

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.3