Packages, Kernels, and Extensions

Table of Contents:


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
biopython Freely available Python tools for computational molecular biology
bokeh Interactive visualization library for Python that enables beautiful and meaningful visual presentation of data in modern web browsers


Clone of CCAL ( with calls to R removed


In this library, you can find many (hopefully good) functions intended to be a support library for GenePattern.
cyjupyter Cytoscape.js network visualization widget for Jupyter Notebook
dcplib Modules shared among multiple Data Coordination Platform components
genefab GeneLab ( API wrapper


GenePattern Notebook extension for Jupyter


This is a Python library for working with GenePattern programmatically. Behind the scenes, calls from this library execute the GenePattern REST API.
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).
humanfriendly Human friendly output for text interfaces using Python


Jupyter extension for embedding the igv.js genome visualization in a notebook
ipywidgets IPython HTML widgets for Jupyter


WYSIWYG editing functionality for markdown/HTML cells in Jupyter
louvain Louvain is a general algorithm for methods of community detection in large networks.
matplotlib Matplotlib is a Python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.


Package for creating user-friendly Jupyter notebooks that are accessible to both programming and non-programming users
ndex2 The NDEx2 Python Client provides methods to access NDEx via the NDEx REST Server API.
networkx Python package for creating and manipulating graphs and networks.
numba Numba is an open source, NumPy-aware optimizing compiler for Python.
numpy NumPy is the fundamental package for array computing with Python.
pandas Powerful data structures for data analysis, time series, and statistics
plotly An open-source, interactive graphing library for Python
py2cytoscape Utilities to use Cytoscape and Cytoscape.js from Python
pysam A python module for reading, manipulating and writing genomic data sets
rpy2 Python interface to the R language (embedded R)
scanpy Scalable toolkit for analyzing single-cell gene expression data
scikit-image Image processing routines for SciPy
scikit-learn A set of python modules for machine learning and data mining
scipy SciPy: Scientific Library for Python
seaborn A library for making statistical graphics in Python. It is built on top of matplotlib and closely integrated with pandas data structures.
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.


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