Packages, Kernels, and Extensions

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