Table of Contents:
Packages
These are available in the Python 3.7 kernel
Bold 
packages were developed by the GenePattern Notebook team.
| Name | Description | URL |
|---|---|---|
| anndata | Scalable way of keeping track of data and learning annotations | https://anndata.readthedocs.io/en/stable/ |
| biopython | Freely available Python tools for computational molecular biology | https://biopython.org/ |
| bokeh | Interactive visualization library for Python that enables beautiful and meaningful visual presentation of data in modern web browsers | https://bokeh.org/ |
|
ccalnoir |
Clone of CCAL (https://github.com/UCSD-CCAL/ccal) with calls to R removed | https://github.com/edjuaro/ccal-noir |
|
cuzcatlan |
In this library, you can find many (hopefully good) functions intended to be a support library for GenePattern. | https://github.com/edjuaro/cuzcatlan |
| cyjupyter | Cytoscape.js network visualization widget for Jupyter Notebook | https://github.com/cytoscape/cytoscape-jupyter-widget |
| dcplib | Modules shared among multiple Data Coordination Platform components | https://github.com/HumanCellAtlas/dcplib |
| genefab | GeneLab (https://genelab.nasa.gov/) API wrapper | https://github.com/LankyCyril/genefab |
|
genepattern-notebook |
GenePattern Notebook extension for Jupyter | https://github.com/genepattern/genepattern-notebook |
|
genepattern-python |
This is a Python library for working with GenePattern programmatically. Behind the scenes, calls from this library execute the GenePattern REST API. | https://github.com/genepattern/genepattern-python |
| hca | This repository is a pip installable Command Line Interface (CLI) and Python library (API) for interacting with the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA). | https://github.com/HumanCellAtlas/dcp-cli |
| humanfriendly | Human friendly output for text interfaces using Python | https://humanfriendly.readthedocs.io/en/latest/ |
|
igv-jupyter |
Jupyter extension for embedding the igv.js genome visualization in a notebook | https://github.com/igvteam/igv-jupyter |
| ipywidgets | IPython HTML widgets for Jupyter | http://ipython.org/ |
|
jupyter-wysiwyg |
WYSIWYG editing functionality for markdown/HTML cells in Jupyter | https://github.com/genepattern/jupyter-wysiwyg/ |
| louvain | Louvain is a general algorithm for methods of community detection in large networks. | https://github.com/vtraag/louvain-igraph |
| matplotlib | Matplotlib is a Python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. | https://matplotlib.org/ |
|
nbtools |
Package for creating user-friendly Jupyter notebooks that are accessible to both programming and non-programming users | https://github.com/genepattern/nbtools |
| ndex2 | The NDEx2 Python Client provides methods to access NDEx via the NDEx REST Server API. | https://github.com/ndexbio/ndex2-client |
| networkx | Python package for creating and manipulating graphs and networks. | http://networkx.github.io/ |
| numba | Numba is an open source, NumPy-aware optimizing compiler for Python. | http://numba.pydata.org/ |
| numpy | NumPy is the fundamental package for array computing with Python. | https://numpy.org/ |
| pandas | Powerful data structures for data analysis, time series, and statistics | https://pandas.pydata.org/ |
| plotly | An open-source, interactive graphing library for Python | https://plot.ly/python/ |
| py2cytoscape | Utilities to use Cytoscape and Cytoscape.js from Python | https://github.com/cytoscape/py2cytoscape |
| pysam | A python module for reading, manipulating and writing genomic data sets | https://github.com/pysam-developers/pysam |
| rpy2 | Python interface to the R language (embedded R) | https://rpy2.bitbucket.io/ |
| scanpy | Scalable toolkit for analyzing single-cell gene expression data | https://github.com/theislab/scanpy |
| scikit-image | Image processing routines for SciPy | https://scikit-image.org/ |
| scikit-learn | A set of python modules for machine learning and data mining | https://scikit-learn.org/stable/ |
| scipy | SciPy: Scientific Library for Python | https://www.scipy.org/ |
| seaborn | A library for making statistical graphics in Python. It is built on top of matplotlib and closely integrated with pandas data structures. | https://seaborn.pydata.org/ |
| umap-learn | Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. | https://github.com/lmcinnes/umap |
Kernels
| python3.6 | GenePattern Notebook Python 3.6 kernel |
| python3.7 | GenePattern Notebook Python 3.7 kernel (default) |
| r3.6 | GenePattern Notebook R 3.6 kernel |
Jupyter Extensions
| collapsible_headings |
| cytoscape-jupyter-widget |
|
genepattern |
|
jupyter_wysiwyg |
|
nbtools |
| toc2 |
| jupyter-js-widgets |
|
repo |
|
igv-jupyter |