https://github.com/bnediction/bonesistools
Python package providing bioinformatics tools for upstream and downstream analysis of the BoNesis framework
https://github.com/bnediction/bonesistools
anndata atacseq bioinformatics boolean-networks gene-regulatory-networks mudata python rnaseq single-cell systems-biology
Last synced: 1 day ago
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Python package providing bioinformatics tools for upstream and downstream analysis of the BoNesis framework
- Host: GitHub
- URL: https://github.com/bnediction/bonesistools
- Owner: bnediction
- License: other
- Created: 2025-02-26T02:04:13.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-05-31T01:37:10.000Z (13 days ago)
- Last Synced: 2026-06-08T02:33:20.902Z (5 days ago)
- Topics: anndata, atacseq, bioinformatics, boolean-networks, gene-regulatory-networks, mudata, python, rnaseq, single-cell, systems-biology
- Language: Python
- Homepage:
- Size: 10.5 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# BoNesisTools
`BoNesisTools` provides Python-implemented toolkits for upstream and downstream analyses around the [BoNesis](https://github.com/bnediction/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
```python
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](https://github.com/scverse/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`
- embedding, density, composition and graph visualizations
- distribution 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:
```python
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
- HCOP: `bt.dbs.hcop`
- orthology mappings
Example:
```python
genesyn = bt.dbs.ncbi.genesyn()
grn = bt.dbs.omnipath.collectri(
organism="mouse",
genesyn=genesyn,
)
```
---
## Installation
Install the latest release:
```sh
pip install bonesistools
```
Install the single-cell dependencies:
```sh
pip install "bonesistools[sctools]"
```
Install all optional dependencies:
```sh
pip install "bonesistools[all]"
```
Install the development version:
```sh
git clone https://github.com/bnediction/bonesistools.git
cd bonesistools
pip install -e ".[all]"
```
or directly:
```sh
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](http://www.cecill.info/index.en.html) 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/