Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: Newgene

gravatar for Newgene
Newgene • 350
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
Email:
a*******@yahoo.com

Posts by Newgene

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
317
views
1
answers
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 Newgene • 350
3
votes
2
answers
850
views
2
answers
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 Newgene • 350
1
vote
1
answer
2.3k
views
1
answers
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 Newgene • 350
0
votes
1
answer
988
views
1
answers
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 Newgene • 350
1
vote
1
answer
988
views
1
answers
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 Newgene • 350
2
votes
3
answers
2.8k
views
3
answers
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 Newgene • 350
4
votes
2
answers
3.6k
views
2
answers
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 Newgene • 350
6
votes
2
answers
10k
views
2
answers
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 Newgene • 350
3
votes
3
answers
4.9k
views
3
answers
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 Newgene • 350
4
votes
3
answers
12k
views
3
answers
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 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
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1516 users visited in the last hour
_