[IPython-dev] ANN: GenePattern Notebook released
Thorin Tabor
thorin at broadinstitute.org
Fri Aug 5 16:16:10 EDT 2016
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
<http://genepattern.org/genepattern-notebooks>
https://github.com/genepattern/genepattern-notebook
<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
<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 <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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