BoNesisTools

BoNesisTools provides Python-implemented toolkits for upstream and downstream analyses around the BoNesis ecosystem.

The package provides:

• Boolean algebra and partial Boolean abstractions
• Boolean network manipulation and analysis
• signed influence graph utilities
• GRN-informed Boolean predecessor inference
• single-cell and multimodal analysis helpers
• biological database interfaces

Usage

import bonesistools as bt

BoNesisTools exposes four main namespaces:

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

---

Single-cell tools

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

Submodules:

• preprocessing: bt.sct.pp

  • gene name harmonization
  • metadata transfer utilities
  • lightweight preprocessing helpers

• tools: bt.sct.tl

  • K-nearest-neighbor and shared-neighbor graph utilities
  • marker and log-fold-change analysis
  • regression and matrix conversion utilities

• plotting: bt.sct.pl

  • scatter, density and graph visualizations
  • boxplot and embedding utilities

• datasets: bt.sct.datasets

  • packaged reference datasets

---

Boolean modelling utilities

bt.bpy provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.

Submodules:

• Boolean algebra: bt.bpy.ba

  • partial Boolean abstractions and hypercube representations
  • Boolean differential and predecessor inference utilities

• Boolean network: bt.bpy.bn

  • Boolean network manipulation and analysis
  • fixed-point computation
  • .bnet import/export

• influence graph: bt.bpy.ig

  • signed regulatory influence graphs
  • feedback circuit and SCC analysis
  • signed interaction scoring from bounded walks
  • graph compression and visualization utilities

Example:

bn = bt.bpy.bn.BooleanNetwork(
    {
        "A": "B & ~C",
        "B": 1,
        "C": 0,
    }
)

graph = bn.to_influence_graph()

graph.show()

---

Biological external resources

bt.dbs provides lightweight interfaces and utilities for biological external resources.

Submodules:

• NCBI: bt.dbs.ncbi

  • gene synonym harmonization
  • gene annotation utilities

• OmniPath: bt.dbs.omnipath

  • DoRothEA transcription factor interactions
  • CollecTRI regulatory interaction networks

Example:

genesyn = bt.dbs.ncbi.GeneSynonyms()

grn = bt.dbs.omnipath.load_collectri_grn(
    organism="mouse",
    genesyn=genesyn,
)

---

Installation

Install the latest release:

pip install bonesistools

Install the single-cell dependencies:

pip install "bonesistools[sctools]"

Install all optional 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 bugs or ask questions here:

https://github.com/bnediction/bonesistools/issues

---

License

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

This package also includes third-party data resources derived from the NCBI Gene database (gene_info). NCBI places no restrictions on the use or redistribution of these data: https://www.ncbi.nlm.nih.gov/home/about/policies/