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BoNesisTools\n\n`BoNesisTools` provides Python-implemented toolkits for upstream and downstream analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.\n\nThe package provides:\n\n- Boolean algebra and partial Boolean abstractions\n- Boolean network manipulation and analysis\n- signed influence graph utilities\n- GRN-informed Boolean predecessor inference\n- single-cell and multimodal analysis helpers\n- biological database interfaces\n\n## Usage\n\n```python\nimport bonesistools as bt\n```\n\n`BoNesisTools` exposes four main namespaces:\n\n- `bt.sct` — single-cell and multimodal annotated data tools\n- `bt.bpy` — Boolean modelling and graph utilities\n- `bt.dbs` — biological database interfaces\n- `bt.grn` — deprecated alias for `bt.bpy.ig`\n\n---\n\n## Single-cell tools\n\n`bt.sct` follows a [Scanpy](https://github.com/scverse/scanpy)-like API while providing additional and complementary features for single-cell analyses.\n\nSubmodules:\n\n- preprocessing: `bt.sct.pp`\n  - gene name harmonization\n  - metadata transfer utilities\n  - lightweight preprocessing helpers\n\n- tools: `bt.sct.tl`\n  - K-nearest-neighbor and shared-neighbor graph utilities\n  - marker and log-fold-change analysis\n  - regression and matrix conversion utilities\n\n- plotting: `bt.sct.pl`\n  - embedding, density, composition and graph visualizations\n  - distribution utilities\n\n- datasets: `bt.sct.datasets`\n  - packaged reference datasets\n\n---\n\n## Boolean modelling utilities\n\n`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.\n\nSubmodules:\n\n- Boolean algebra: `bt.bpy.ba`\n  - partial Boolean abstractions and hypercube representations\n  - Boolean differential and predecessor inference utilities\n\n- Boolean network: `bt.bpy.bn`\n  - Boolean network manipulation and analysis\n  - fixed-point computation\n  - `.bnet` import/export\n\n- influence graph: `bt.bpy.ig`\n  - signed regulatory influence graphs\n  - feedback circuit and SCC analysis\n  - signed interaction scoring from bounded walks\n  - graph compression and visualization utilities\n\nExample:\n\n```python\nbn = bt.bpy.bn.BooleanNetwork(\n    {\n        \"A\": \"B \u0026 ~C\",\n        \"B\": 1,\n        \"C\": 0,\n    }\n)\n\ngraph = bn.to_influence_graph()\n\ngraph.show()\n```\n\n---\n\n## Biological external resources\n\n`bt.dbs` provides lightweight interfaces and utilities for biological\nexternal resources.\n\nSubmodules:\n\n- NCBI: `bt.dbs.ncbi`\n  - gene synonym harmonization\n  - gene annotation utilities\n\n- OmniPath: `bt.dbs.omnipath`\n  - DoRothEA transcription factor interactions\n  - CollecTRI regulatory interaction networks\n\n- HCOP: `bt.dbs.hcop`\n  - orthology mappings\n\nExample:\n\n```python\ngenesyn = bt.dbs.ncbi.genesyn()\n\ngrn = bt.dbs.omnipath.collectri(\n    organism=\"mouse\",\n    genesyn=genesyn,\n)\n```\n\n---\n\n## Installation\n\nInstall the latest release:\n\n```sh\npip install bonesistools\n```\n\nInstall the single-cell dependencies:\n\n```sh\npip install \"bonesistools[sctools]\"\n```\n\nInstall all optional dependencies:\n\n```sh\npip install \"bonesistools[all]\"\n```\n\nInstall the development version:\n\n```sh\ngit clone https://github.com/bnediction/bonesistools.git\ncd bonesistools\npip install -e \".[all]\"\n```\n\nor directly:\n\n```sh\npip install git+https://github.com/bnediction/bonesistools.git\n```\n\n---\n\n## Bugs\n\nPlease report bugs or ask questions here:\n\nhttps://github.com/bnediction/bonesistools/issues\n\n---\n\n## License\n\nThis package is distributed under the [CeCILL v2.1](http://www.cecill.info/index.en.html) free software license (GNU GPL compatible).\n\nThis package also includes third-party data resources derived from the\nNCBI Gene database (`gene_info`). NCBI places no restrictions on the\nuse or redistribution of these data: https://www.ncbi.nlm.nih.gov/home/about/policies/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbnediction%2Fbonesistools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbnediction%2Fbonesistools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbnediction%2Fbonesistools/lists"}