Third-party packages

This page lists third-party packages/modules built upon MyGene.info services.

MyGene python module

“mygene” is an easy-to-use Python wrapper to access MyGene.info services.

You can install it easily using either pip or easy_install:

pip install mygene               #this is preferred

or:

easy_install mygene

This is a brief example:

In [1]: import mygene

In [2]: mg = mygene.MyGeneInfo()

In [3]: mg.getgene(1017)
Out[3]:
{'_id': '1017',
 'entrezgene': 1017,
 'name': 'cyclin-dependent kinase 2',
 'symbol': 'CDK2',
 'taxid': 9606}

In [4]:  mg.query('cdk2', size=2)
Out[4]:
{'hits': [{'_id': '1017',
   '_score': 373.24667,
   'entrezgene': 1017,
   'name': 'cyclin-dependent kinase 2',
   'symbol': 'CDK2',
   'taxid': 9606},
  {'_id': '12566',
   '_score': 353.90176,
   'entrezgene': 12566,
   'name': 'cyclin-dependent kinase 2',
   'symbol': 'Cdk2',
   'taxid': 10090}],
 'max_score': 373.24667,
 'took': 10,
 'total': 28}

See https://pypi.python.org/pypi/mygene for more details.

MyGene R package

An R wrapper for the MyGene.info API is available in Bioconductor since v3.0. To install:

source("https://bioconductor.org/biocLite.R")
biocLite("mygene")

To view documentation for your installation, enter R and type:

browseVignettes("mygene")

For more information, visit the Bioconductor mygene page.

MyGene autocomplete widget

This autocomplete widget for gene query (built upon JQueryUI’s autocomplete widget) provides suggestions while you type a gene symbol or name into the field. You can easily embed it into your web application. It also provides many customization options for your different use-cases.

See https://bitbucket.org/sulab/mygene.autocomplete/overview for more details.

You can also play with this jsFiddle example:

Another MyGene Python wrapper

This is yet another Python wrapper of MyGene.info services created by Brian Schrader. It’s hosted at https://github.com/Sonictherocketman/mygene-api.

It’s available from PyPI as well:

pip install mygene-api

Some basic examples:

  • Find a given gene with the id: CDK2.

""" Use the query API to find a gene with
the given symbol.
"""
from mygene.gene import Gene

results = Gene.find_by(q='CDK2')
for r in result:
    print r._id, r.name

>>> 1017 cyclin-dependent kinase 2
12566 cyclin-dependent kinase 2
362817 cyclin dependent kinase 2
52004 CDK2-associated protein 2
...

  • Given an known gene, get it’s begin and end coordinates.

""" Use the annotation API to find the full
details of a given gene.
"""
from mygene.gene import gene

gene = Gene.get('1017')
print gene._id, gene.genomic_pos_hg19['start'], gene.genomic_pos_hg19['end']

>>> 1017 56360553 56366568

  • This library also supports the metadata API.

from mygene.metadata import Metadata

metadata = Metadata.get_metadata()
print metadata.stats['total_genes']

>>> 12611464