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refactor: set up gene-alias pairs dataset #14

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refactor: set up gene-alias pairs dataset #14

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anastasiabratulin
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@anastasiabratulin anastasiabratulin commented Aug 29, 2024 •
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  • created a gene-alias pair capture nb
  • ran analysis using updated info from ENSG, HGNC, and NCBI
  • split out DGIdb analyses from monster nb
  • added the alias-primary analysis nb

@anastasiabratulin
add function to create collision records with gene symbol and ensg id
c25c665
@anastasiabratulin
changed the create yaml function to put new ones in a folder
9e37997
@anastasiabratulin
updated hgnc and ensg downloads
c63ad9c
@anastasiabratulin
split out dgidb_claims_analysis from total_alias_overlap nb
1be793c
@anastasiabratulin
analyze ambiguous symbol usag in pubmed abstracts
46d3689
@anastasiabratulin
add analysis on dgidb queries
038be61
@anastasiabratulin
remove dgidb_claim_analysis from this notebook
2692bd1
@anastasiabratulin
reorganized files
4ba8926
@anastasiabratulin
added TR2 collision record
7878cf6
@anastasiabratulin
added alias-primary analysis notebook
18c3367
@anastasiabratulin
change file organization
06b4b75
@anastasiabratulin
split out collision record generation from alias-alias collision anal…
d2514df 
…ysis nb
@anastasiabratulin
concept-alias pair count added to alias-alias collision analysis nb
cd1ecc9
@anastasiabratulin
Fixed and ran the collision record generation notebook
43d124b
@anastasiabratulin
corrected collision record generation nb -records contain associated …
e749263 
…genes from all sources + associated data order is preserved so that it can be connected back to the associated genes
@anastasiabratulin
add fields in collision record generator nb for collision gene relati…
3b0f262 
…onship details
@anastasiabratulin anastasiabratulin self-assigned this Aug 29, 2024
@anastasiabratulin anastasiabratulin changed the title Issue 7 refactor: set up collision record generator Aug 29, 2024
korikuzma
korikuzma reviewed Aug 30, 2024
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@korikuzma korikuzma left a comment •
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Considering the amount of files you're generating (and future files that will be added), it might be good to store these in a public s3 bucket. If you want a test file so others can see what the format looks like, I think that would make sense.

@anastasiabratulin anastasiabratulin changed the title refactor: set up collision record generator refactor: set up gene-alias pairs dataset Nov 4, 2024
@anastasiabratulin anastasiabratulin marked this pull request as ready for review November 7, 2024 19:38
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@jsstevenson jsstevenson Awaiting requested review from jsstevenson

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@anastasiabratulin @korikuzma