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<p>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.<br>
<br>
<a href="http://genepattern.org/genepattern-notebooks"
rel="noreferrer" target="_blank">http://genepattern.org/genepat<wbr>tern-notebooks</a><br>
<a href="https://github.com/genepattern/genepattern-notebook"
rel="noreferrer" target="_blank">https://github.com/genepattern<wbr>/genepattern-notebook</a><br>
<br>
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.<br>
<br>
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.<br>
<br>
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:<br>
<br>
<a
href="http://genepattern.org/using-the-genepattern-notebook-environment"
rel="noreferrer" target="_blank">http://genepattern.org/using-t<wbr>he-genepattern-notebook-enviro<wbr>nment</a><br>
<br>
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.<br>
<br>
<a href="https://notebook.genepattern.org" rel="noreferrer"
target="_blank">https://notebook.genepattern.o<wbr>rg</a><br>
<br>
The GenePattern Notebook extension can also be easily installed
from pip or conda:<br>
<br>
pip install genepattern-notebook<br>
<br>
or<br>
<br>
conda install -c genepattern genepattern-notebook<br>
<br>
Once installed, you will need to install and enable the
accompanying server and nbextensions. The ipywidgets nbextension
must also be enabled:<br>
<br>
jupyter nbextension enable --py widgetsnbextension<br>
jupyter nbextension install --py genepattern<br>
jupyter nbextension enable --py genepattern<br>
jupyter serverextension enable --py genepattern<br>
<br>
The GenePattern Notebook extension supports both Python 3.3+ and
Python 2.7.<br>
<br>
Cheers!<br>
The GenePattern Team</p>
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