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[FEAT] Protein AccNum mapping #109

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Klangina opened this issue Oct 23, 2024 Discussed in #24 · 3 comments
Open
3 tasks

[FEAT] Protein AccNum mapping #109

Klangina opened this issue Oct 23, 2024 Discussed in #24 · 3 comments
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@Klangina
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bioinfo Bioinformatics related enhancement New feature or request outreachy for outreachy interns
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v0 | short-term f...

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@Klangina
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Klangina commented Oct 23, 2024 •
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Discussed in #24

Originally posted by jananiravi July 14, 2024

  • from UniProt to NCBI | up2ncbi
  • NCBI to UniProt | ncbi2up
  • Protein to IPG | acc2ipg

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@jananiravi @epbrenner : Is it okay if I use the following package?

Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 23, 2024
@Klangina
Issue-JRaviLab#109 a:
a4c01c1 
- Created R/accnum.R
- Added up2ncbi
-  Added documentation in roxygen
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 23, 2024
@Klangina
Issue-JRaviLab#109-b:
9bc2ded 
- Added ncbi2up to  R/accnum.R
-  Added documentation in roxygen
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Potentially yes, but make sure it will work for all species mapping, not just human (Hs). rentrez might be a good package to start with, but I'm sure there are others too that connect ncbi and uniprot. @epbrenner have you used this one?

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I have created a PR with HS genes yesterday. I will look into rentrez and create another pr for that. Any issues/cons of rentrez that's there from the top of your mind?
@jananiravi @epbrenner

@jananiravi jananiravi added enhancement New feature or request outreachy for outreachy interns bioinfo Bioinformatics related labels Oct 26, 2024
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bioinfo Bioinformatics related enhancement New feature or request outreachy for outreachy interns
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v0 | short-term fixes
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