We are pleased to announce the release of GenePattern Notebook, an
extension for Jupyter which provides access to hundreds of different
bioinformatic analyses through the GenePattern web service.
http://genepattern.org/genepattern-notebooks
https://github.com/genepattern/genepattern-notebook
Supported analyses include machine learning algorithms (clustering,
classification, dimension reduction), tools for working with gene
expression data (both RNA-seq and microarray), sequence variation and copy
number analysis, proteomics, flow cytometry and network analysis.
Included in the extension are visual widgets for running analyses, tools
for sending results to downstream steps in a bioinformatic workflow,
Jupyter magics for creating GenePattern widgets and a Python library for
programmatically working with your results.
To get started after installing the extension, just open a notebook and
change a cell to the new GenePattern cell type. A full walk-through of
using the extension is available on our website:
http://genepattern.org/using-the-genepattern-notebook-environment
An early version of the GenePattern Notebook Repository, a service
providing access to GenePattern Notebook functionality as well as a variety
of example notebooks, is available at the address below.
https://notebook.genepattern.org
The GenePattern Notebook extension can also be easily installed from pip or
conda:
pip install genepattern-notebook
or
conda install -c genepattern genepattern-notebook
Once installed, you will need to install and enable the accompanying server
and nbextensions. The ipywidgets nbextension must also be enabled:
jupyter nbextension enable --py widgetsnbextension
jupyter nbextension install --py genepattern
jupyter nbextension enable --py genepattern
jupyter serverextension enable --py genepattern
The GenePattern Notebook extension supports both Python 3.3+ and Python 2.7.
Cheers!
The GenePattern Team
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