bonesistools 1.3.0

Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework

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

---

Single-cell tools

bt.sct is inspired by Scanpy while providing additional and complementary features for single-cell analyses.

Submodules:

• preprocessing: bt.sct.pp

  • expression transformations, feature selection, filtering and metadata utilities

• tools: bt.sct.tl

  • embeddings, neighborhood graphs, clustering, differential analysis and matrix utilities

• plotting: bt.sct.pl

  • visualization helpers for embeddings, trajectories, distributions and summaries

• datasets: bt.sct.datasets

  • registered single-cell example datasets loaded with bt.sct.datasets.load(...)

Example:

bt.sct.datasets.available()
bt.sct.datasets.info("pbmc3k")
adata = bt.sct.datasets.load("pbmc3k")
adata = bt.sct.datasets.load("nestorowa")
bt.sct.datasets.clear("pbmc3k")

---

Boolean modelling utilities

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

Submodules:

• Boolean algebra: bt.bpy.ba

  • logical objects and transformations for Boolean-state reasoning

• Boolean network: bt.bpy.bn

  • Boolean model representation, conversion, analysis and exchange

• influence graph: bt.bpy.ig

  • signed regulatory graph construction, comparison, analysis and display

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 identifier, synonym and annotation utilities

• OmniPath: bt.dbs.omnipath

  • regulatory interaction datasets

• HCOP: bt.dbs.hcop

  • orthology resources

Example:

genesyn = bt.dbs.ncbi.genesyn()

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

---

Installation

Install the latest release:

pip install bonesistools

Install the omics dependencies:

pip install "bonesistools[omics]"

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/