BoNesisTools

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

Functionalities

BoNesisTools contains multiple sub-packages:

• sctools (operations on unimodal and multimodal annotated data)
• boolpy (features for Boolean algebra and Boolean functions)
• grntools (efficient features and algorithms for gene regulatory network-like graphs)
• databases (information requests to bioinformatics databases)

Note that sctools proposes a wide range of efficient features that are not available in Scanpy and muon packages.

Installation

Install the latest released version of BoNesisTools with pip:

pip install bonesistools

Install with all optional dependencies:

pip install bonesistools[default]

for the development version, use:

git clone https://github.com/bnediction/bonesistools.git

or:

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

Usage

For importing package:

import bonesistools as bt

Each sub-package has a corresponding alias:

• sctools can be accessed with bt.sct, which is decomposed into three Scanpy-like parts: preprocessing (bt.sct.pp), tools (bt.sct.tl) and plotting (bt.sct.pl)
• boolpy can be accessed with bt.bpy
• grntools can be accessed with bt.grn
• databases can be accessed with bt.dbs, which is decomposed into two parts for the moment: ncbi (bt.dbs.ncbi) for handling gene alias-related issues and CollecTRI (bt.dbs.collectri) for getting a gene regulatory networks

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).