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bioservices

Access to Biological Web Services from Python.

clusterdbanalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

cmonkey2

Python port of cMonkey, a machine-learning based method for clustering

cmonkey2-tools

Python tools and notebooks for running, using, and exploring results of cMonkey2 runs

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

easygui

easygui for Python

ete

ETE is a Python programming toolkit for building, comparing, annotating, manipulating and visualising trees. It provides both a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

github-cheat-sheet

A list of cool features of Git and GitHub.

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

httpdomain

Documenting RESTful HTTP APIs

inferelator

The official Inferelator repository maintained by current or former Bonneau lab members

josephryanpeterson.github.io

jsonmodels

jsonmodels is library to make it easier for you to deal with structures that are converted to, or read from JSON.

mminte

napoleon

perfectbru

Plan your perfect brew

plogp_trn

Reconstruct a Transcriptional Regulatory Network using the principle of Maximum Entropy.

pydcemri

Python module for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data

pydicom

Read, modify and write DICOM files with python code

pyvenn

2 ~ 6 sets venn diagram for python

pyveplot

SVG Hiveplot Python API

spacker

Pack a set of spheres into an object

tifffile

Read and write TIFF(r) files. Forked from https://pypi.org/project/tifffile

varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

vivarium

a multi-scale simulation platform for whole-cell modeling