User: Newgene
Newgene • 350
- Reputation:
- 350
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- Trusted
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- United States
- Website:
- https://wulab.io/
- Twitter:
- chunleiwu
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 10 years, 1 month ago
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- a*******@yahoo.com
Posts by Newgene
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... As answered in [this github issue][1], the [current myvariant batch query][2] does not support this kind of batch query (requiring to query the combination of multiple fields). You can always make such query via GET for a single query.
But this does represent a very useful use case we would like to ...
written 18 months ago by
Newgene • 350
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... Hi @manu.tiwari, [MyGene.info][1] API (the web API underlying the mygene R package) is keeping updated from NCBI, Ensembl, UCSC and many other resources. For example, Ensembl data were updated to version 89; UCSC data were updated on 20170608. So the *Drosophila melanogaster* annotation data from My ...
written 3.7 years ago by
Newgene • 350
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... Getting gene symbol/name from a given gene id is fairly straightforward. One easy option is to use MyGene.info web API:
http://mygene.info/v3/gene/1017?fields=symbol,name
where 1017 is your gene id. It can also be done via mygene Python module:
https://pypi.python.org/pypi/mygene
I think you jus ...
written 4.6 years ago by
Newgene • 350
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... also see this related post:
https://www.biostars.org/p/200203/#203836
...
written 4.6 years ago by
Newgene • 350
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... Try MyVariant.info API:
http://myvariant.info/v1/query?q=rs4340&fields=clinvar
Batch is supported via POST. Also the Python or R clients:
https://pypi.python.org/pypi/myvariant
https://www.bioconductor.org/packages/release/bioc/html/myvariant.html
...
written 4.6 years ago by
Newgene • 350
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... Try [MyVariant.info](http://myvariant.info) API:
http://myvariant.info/v1/query?q=dbsnp.rsid:rs727503873&fields=clinvar
There is a "variant_id" field under "clinvar". Or maybe you don't need variant_id anymore, since you can get back ClinVar annotations from a rsid directly now.
Check out thi ...
written 4.6 years ago by
Newgene • 350
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... [MyVariant.info](http://myvariant.info) API is very handy for this type of queries. Given a rsid to get the ClinVar annotation:
http://myvariant.info/v1/query?q=rs727503873&fields=clinvar
or more explicitly:
http://myvariant.info/v1/query?q=dbsnp.rsid:rs727503873&fields=clinvar
Batch que ...
written 4.6 years ago by
Newgene • 350
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... MyGene.info API, or their Python/R clients:
https://pypi.python.org/pypi/mygene/
http://bioconductor.org/packages/release/bioc/html/mygene.html
A tutorial here: http://nbviewer.jupyter.org/gist/newgene/6771106
...
written 4.6 years ago by
Newgene • 350
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... use MyGene.info API, python and R clients are available.
For Python:
pip install mygene
then
import mygene
mg = mygene.MyGeneInfo()
mg.querymany(['NM_008866','NM_011541','NM_011011'], scopes='refseq')
that's it!
...
written 4.6 years ago by
Newgene • 350
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... It's easy to do that using [mygene](https://pypi.python.org/pypi/mygene) Python module:
import mygene
mg = mygene.MyGeneInfo()
mg.querymany(ens, scopes='ensembl.transcript')
That's it!
...
written 4.6 years ago by
Newgene • 350
Latest awards to Newgene
Commentator
2.0 years ago,
created a comment with at least 3 up-votes.
For C: Convert gene name to uniprot ID
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For A: convert gene name to entrez id
Good Answer
3.7 years ago,
created an answer that was upvoted at least 5 times.
For A: convert gene name to entrez id
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: myGene in R using different genome assembly
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: Searching for ClinVar entries based on SNP annotation
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Pyt
Teacher
4.6 years ago,
created an answer with at least 3 up-votes.
For A: Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Pyt
Teacher
4.6 years ago,
created an answer with at least 3 up-votes.
For A: Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Pyt
Teacher
4.6 years ago,
created an answer with at least 3 up-votes.
For A: Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Pyt
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