bonesistools 1.2.0

BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework

BoNesisTools

BoNesisTools is a Python package providing bioinformatics utilities for upstream and downstream analyses of the BoNesis framework.

Usage

import bonesistools as bt

BoNesisTools exposes four main namespaces:

• bt.sct — single-cell and multimodal annotated data tools
• bt.bpy — Boolean modelling utilities
• bt.dbs — biological database interfaces
• bt.grn — deprecated alias for bt.bpy.ig

bt.sct follows a Scanpy-like API while providing additional and complementary features for single-cell analyses:

• preprocessing: bt.sct.pp
• tools: bt.sct.tl
• plotting: bt.sct.pl
• datasets: bt.sct.datasets

bt.bpy provides utilities for Boolean modelling:

• Boolean algebra and partial Boolean abstractions: bt.bpy.ba
• Boolean network utilities: bt.bpy.bn
• interaction and influence graph utilities: bt.bpy.ig

Installation

Install the latest release:

pip install bonesistools

Install the single-cell tools dependencies:

pip install "bonesistools[sctools]"

Install with all extra dependencies:

pip install "bonesistools[all]"

Install the development version:

git clone https://github.com/bnediction/bonesistools.git
cd bonesistools
pip install -e ".[all]"

or directly:

pip install git+https://github.com/bnediction/bonesistools.git

Bugs

Please report any bugs or ask questions here.

License

This package is distributed under the CeCILL v2.1 free software license (GNU GPL compatible).