User: Newgene

gravatar for Newgene
Newgene350
Reputation:
350
Status:
Trusted
Location:
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

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Batch Query MyVariant.info with chr:pos list
... 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 Newgene350
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Answer: A: myGene in R using different genome assembly
... 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 Newgene350
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Answer: A: Python scripting for adding gene name into gff annotation file
... 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 Newgene350
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Comment: C: Connection timeout when using multiple commands on eutils
... also see this related post: https://www.biostars.org/p/200203/#203836 ...
written 4.6 years ago by Newgene350
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Answer: A: Connection timeout when using multiple commands on eutils
... 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 Newgene350
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Answer: A: How to change snp ID to Variation ID of Clinvar Database
... 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 Newgene350
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Answer: A: Searching for ClinVar entries based on SNP annotation
... [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 Newgene350
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Answer: A: convert gene name to entrez id
... 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 Newgene350
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Answer: A: How To Convert Refseq Id To Gene Symbol As Pitx1
... 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 Newgene350
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Answer: A: Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Pyt
... 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 Newgene350

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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