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.

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

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

Please report any bugs or ask questions here.

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