| 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 |