omicsync 0.1.0__tar.gz

omicsync-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Paterson V.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

omicsync-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: omicsync
+Version: 0.1.0
+Summary: Multi-omics data harmonisation for Python
+Author-email: "Paterson V." <citrus.bird72@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2026 Paterson V.
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/vi-c-ky/omicsync
+Project-URL: Documentation, https://github.com/vi-c-ky/omicsync/blob/main/docs/index.md
+Project-URL: Repository, https://github.com/vi-c-ky/omicsync
+Project-URL: Bug Tracker, https://github.com/vi-c-ky/omicsync/issues
+Keywords: bioinformatics,multi-omics,TCGA,genomics,data harmonisation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.5.0
+Requires-Dist: numpy>=1.23.0
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: scikit-learn>=1.1.0
+Requires-Dist: requests>=2.28.0
+Provides-Extra: mofa
+Requires-Dist: mofapy2>=0.7.0; extra == "mofa"
+Provides-Extra: geo
+Requires-Dist: GEOparse>=2.0.0; extra == "geo"
+Provides-Extra: torch
+Requires-Dist: torch>=1.12.0; extra == "torch"
+Provides-Extra: anndata
+Requires-Dist: anndata>=0.8.0; extra == "anndata"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: black>=23.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: build>=1.0.0; extra == "dev"
+Requires-Dist: twine>=4.0.0; extra == "dev"
+Provides-Extra: all
+Requires-Dist: omicsync[anndata,geo,mofa,torch]; extra == "all"
+Dynamic: license-file
+
+# omicsync
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+[![PyPI version](https://img.shields.io/pypi/v/omicsync.svg)](https://pypi.org/project/omicsync/)
+
+**A Python library for multi-omics data harmonisation.**
+
+omicsync handles the tedious work of aligning sample IDs, normalising each modality consistently, and exporting to downstream tools so you can focus on biology, not data wrangling.
+
+---
+
+## Installation
+
+```bash
+pip install omicsync
+```
+
+With optional extras:
+
+```bash
+pip install "omicsync[mofa]"       # MOFA2 factor analysis
+pip install "omicsync[geo]"        # GEO data loading
+pip install "omicsync[anndata]"    # AnnData export
+pip install "omicsync[torch]"      # PyTorch tensor export
+pip install "omicsync[all]"        # Everything
+```
+
+---
+
+## Quick Start
+
+```python
+import omicsync as oms
+from omicsync.loaders.csv import load_multimodal_csv
+
+# Load multiple modalities from CSV files
+dataset = load_multimodal_csv({
+    "rna":     "brca_rna.tsv",
+    "protein": "brca_rppa.tsv",
+    "cnv":     "brca_cnv.tsv",
+}, study_id="TCGA-BRCA")
+
+# Align, normalise, filter — all chainable
+dataset.align_samples().normalize().filter_features(min_variance=0.01)
+
+# Export to DataFrame or MOFA2
+df = dataset.to_dataframe()          # samples × features, prefixed columns
+mofa_input = dataset.to_mofa2()      # dict ready for mofapy2 entry_point
+```
+
+---
+
+## Features
+
+- **Sample harmonisation** — TCGA barcode parsing, fuzzy ID matching, coverage reporting
+- **Per-modality normalisation** — auto-detection of count/TPM/M-value formats
+- **Chainable API** — `dataset.align().normalize().filter_features()`
+- **sklearn compatibility** — use `OmicsSyncTransformer` in a `Pipeline`
+- **Multiple export formats** — DataFrame, dict, MOFA2, PyTorch tensor, AnnData
+- **Open Targets integration** — query target-disease associations via GraphQL
+- **Type hints throughout** — fully typed public API
+
+---
+
+## Supported Data Sources
+
+| Source | Loader | Notes |
+|--------|--------|-------|
+| TCGA | `load_tcga_files()` | Local files; barcode auto-harmonisation |
+| GEO | `load_geo()` | Via GEOparse; requires `omicsync[geo]` |
+| CSV/TSV | `load_csv()` | Any tabular file |
+| Open Targets | `load_open_targets_targets()` | GraphQL API v4 |
+
+---
+
+## Supported Modalities
+
+| Modality | Class | Default Normalisation |
+|----------|-------|-----------------------|
+| RNA expression | `RNAModality` | `detect_and_normalise()` (log1p) |
+| DNA methylation | `MethylationModality` | M→beta conversion + clip |
+| Copy number | `CNVModality` | log2 ratio, clipped [-2, 2] |
+| Somatic mutations | `MutationModality` | Binarise at threshold |
+| Protein abundance | `ProteinModality` | Z-score per protein |
+
+---
+
+## Documentation
+
+- [Quickstart guide](docs/quickstart.md)
+- [API reference](docs/api_reference.md)
+- [Tutorial: TCGA BRCA](docs/tutorials/tcga_brca.md)
+- [Tutorial: Custom CSV data](docs/tutorials/custom_data.md)
+
+---
+
+## Citation
+
+If you use omicsync in your research, please cite:
+
+> Paterson V. (2026). *omicsync: A Python library for multi-omics data harmonisation*. GitHub: github.com/vi-c-ky/omicsync
+
+---
+
+## Contributing
+
+Contributions are welcome. Please open an issue or pull request on GitHub.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/my-feature`)
+3. Write tests for new functionality
+4. Run the test suite (`pytest tests/`)
+5. Open a pull request
+
+---
+
+## License
+
+MIT — see [LICENSE](LICENSE) for details.

omicsync-0.1.0/README.md

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+# omicsync
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+[![PyPI version](https://img.shields.io/pypi/v/omicsync.svg)](https://pypi.org/project/omicsync/)
+
+**A Python library for multi-omics data harmonisation.**
+
+omicsync handles the tedious work of aligning sample IDs, normalising each modality consistently, and exporting to downstream tools so you can focus on biology, not data wrangling.
+
+---
+
+## Installation
+
+```bash
+pip install omicsync
+```
+
+With optional extras:
+
+```bash
+pip install "omicsync[mofa]"       # MOFA2 factor analysis
+pip install "omicsync[geo]"        # GEO data loading
+pip install "omicsync[anndata]"    # AnnData export
+pip install "omicsync[torch]"      # PyTorch tensor export
+pip install "omicsync[all]"        # Everything
+```
+
+---
+
+## Quick Start
+
+```python
+import omicsync as oms
+from omicsync.loaders.csv import load_multimodal_csv
+
+# Load multiple modalities from CSV files
+dataset = load_multimodal_csv({
+    "rna":     "brca_rna.tsv",
+    "protein": "brca_rppa.tsv",
+    "cnv":     "brca_cnv.tsv",
+}, study_id="TCGA-BRCA")
+
+# Align, normalise, filter — all chainable
+dataset.align_samples().normalize().filter_features(min_variance=0.01)
+
+# Export to DataFrame or MOFA2
+df = dataset.to_dataframe()          # samples × features, prefixed columns
+mofa_input = dataset.to_mofa2()      # dict ready for mofapy2 entry_point
+```
+
+---
+
+## Features
+
+- **Sample harmonisation** — TCGA barcode parsing, fuzzy ID matching, coverage reporting
+- **Per-modality normalisation** — auto-detection of count/TPM/M-value formats
+- **Chainable API** — `dataset.align().normalize().filter_features()`
+- **sklearn compatibility** — use `OmicsSyncTransformer` in a `Pipeline`
+- **Multiple export formats** — DataFrame, dict, MOFA2, PyTorch tensor, AnnData
+- **Open Targets integration** — query target-disease associations via GraphQL
+- **Type hints throughout** — fully typed public API
+
+---
+
+## Supported Data Sources
+
+| Source | Loader | Notes |
+|--------|--------|-------|
+| TCGA | `load_tcga_files()` | Local files; barcode auto-harmonisation |
+| GEO | `load_geo()` | Via GEOparse; requires `omicsync[geo]` |
+| CSV/TSV | `load_csv()` | Any tabular file |
+| Open Targets | `load_open_targets_targets()` | GraphQL API v4 |
+
+---
+
+## Supported Modalities
+
+| Modality | Class | Default Normalisation |
+|----------|-------|-----------------------|
+| RNA expression | `RNAModality` | `detect_and_normalise()` (log1p) |
+| DNA methylation | `MethylationModality` | M→beta conversion + clip |
+| Copy number | `CNVModality` | log2 ratio, clipped [-2, 2] |
+| Somatic mutations | `MutationModality` | Binarise at threshold |
+| Protein abundance | `ProteinModality` | Z-score per protein |
+
+---
+
+## Documentation
+
+- [Quickstart guide](docs/quickstart.md)
+- [API reference](docs/api_reference.md)
+- [Tutorial: TCGA BRCA](docs/tutorials/tcga_brca.md)
+- [Tutorial: Custom CSV data](docs/tutorials/custom_data.md)
+
+---
+
+## Citation
+
+If you use omicsync in your research, please cite:
+
+> Paterson V. (2026). *omicsync: A Python library for multi-omics data harmonisation*. GitHub: github.com/vi-c-ky/omicsync
+
+---
+
+## Contributing
+
+Contributions are welcome. Please open an issue or pull request on GitHub.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/my-feature`)
+3. Write tests for new functionality
+4. Run the test suite (`pytest tests/`)
+5. Open a pull request
+
+---
+
+## License
+
+MIT — see [LICENSE](LICENSE) for details.

omicsync-0.1.0/omicsync/__init__.py

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+"""omicsync — Multi-omics data harmonisation for Python."""
+
+from omicsync.core.dataset import OmicsDataset
+from omicsync.core.modality import (
+    OmicsModality,
+    RNAModality,
+    MutationModality,
+    MethylationModality,
+    CNVModality,
+    ProteinModality,
+    make_modality,
+)
+from omicsync.core.sample_index import SampleIndex
+from omicsync.utils.logging import set_verbose, get_logger
+
+__version__ = "0.1.0"
+__author__ = "Paterson V."
+__license__ = "MIT"
+
+__all__ = [
+    "__version__",
+    "OmicsDataset",
+    "OmicsModality",
+    "RNAModality",
+    "MutationModality",
+    "MethylationModality",
+    "CNVModality",
+    "ProteinModality",
+    "make_modality",
+    "SampleIndex",
+    "set_verbose",
+    "get_logger",
+]

omicsync-0.1.0/omicsync/core/__init__.py

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+"""Core data structures for omicsync."""
+
+from omicsync.core.dataset import OmicsDataset
+from omicsync.core.modality import (
+    OmicsModality,
+    RNAModality,
+    MutationModality,
+    MethylationModality,
+    CNVModality,
+    ProteinModality,
+    make_modality,
+)
+from omicsync.core.sample_index import SampleIndex
+
+__all__ = [
+    "OmicsDataset",
+    "OmicsModality",
+    "RNAModality",
+    "MutationModality",
+    "MethylationModality",
+    "CNVModality",
+    "ProteinModality",
+    "make_modality",
+    "SampleIndex",
+]